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Yin XN, Wang ZH, Zou L, Yang CW, Shen CY, Liu BK, Yin Y, Liu XJ, Zhang B. Computed tomography radiogenomics: A potential tool for prediction of molecular subtypes in gastric stromal tumor. World J Gastrointest Oncol 2024; 16:1296-1308. [PMID: 38660646 PMCID: PMC11037038 DOI: 10.4251/wjgo.v16.i4.1296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/23/2024] [Accepted: 02/25/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Preoperative knowledge of mutational status of gastrointestinal stromal tumors (GISTs) is essential to guide the individualized precision therapy. AIM To develop a combined model that integrates clinical and contrast-enhanced computed tomography (CE-CT) features to predict gastric GISTs with specific genetic mutations, namely KIT exon 11 mutations or KIT exon 11 codons 557-558 deletions. METHODS A total of 231 GIST patients with definitive genetic phenotypes were divided into a training dataset and a validation dataset in a 7:3 ratio. The models were constructed using selected clinical features, conventional CT features, and radiomics features extracted from abdominal CE-CT images. Three models were developed: ModelCT sign, modelCT sign + rad, and model CTsign + rad + clinic. The diagnostic performance of these models was evaluated using receiver operating characteristic (ROC) curve analysis and the Delong test. RESULTS The ROC analyses revealed that in the training cohort, the area under the curve (AUC) values for modelCT sign, modelCT sign + rad, and modelCT sign + rad + clinic for predicting KIT exon 11 mutation were 0.743, 0.818, and 0.915, respectively. In the validation cohort, the AUC values for the same models were 0.670, 0.781, and 0.811, respectively. For predicting KIT exon 11 codons 557-558 deletions, the AUC values in the training cohort were 0.667, 0.842, and 0.720 for modelCT sign, modelCT sign + rad, and modelCT sign + rad + clinic, respectively. In the validation cohort, the AUC values for the same models were 0.610, 0.782, and 0.795, respectively. Based on the decision curve analysis, it was determined that the modelCT sign + rad + clinic had clinical significance and utility. CONCLUSION Our findings demonstrate that the combined modelCT sign + rad + clinic effectively distinguishes GISTs with KIT exon 11 mutation and KIT exon 11 codons 557-558 deletions. This combined model has the potential to be valuable in assessing the genotype of GISTs.
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Affiliation(s)
- Xiao-Nan Yin
- Gastric Cancer Research Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Zi-Hao Wang
- Gastric Cancer Research Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Li Zou
- Department of Paediatric Surgery, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Cai-Wei Yang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Chao-Yong Shen
- Gastric Cancer Research Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Bai-Ke Liu
- Gastric Cancer Research Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Yuan Yin
- Gastric Cancer Research Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Xi-Jiao Liu
- Department of Radiology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Bo Zhang
- Department of Gastrointestinal Surgery, Sichuan University West China Hospital, Chengdu 610041, Sichuan Province, China
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Molecular Mechanisms of Gastrointestinal Stromal Tumors and Their Impact on Systemic Therapy Decision. Cancers (Basel) 2023; 15:cancers15051498. [PMID: 36900287 PMCID: PMC10001062 DOI: 10.3390/cancers15051498] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are soft tissue sarcomas that mostly derive from Cajal cell precursors. They are by far the most common soft tissue sarcomas. Clinically, they present as gastrointestinal malignancies, most often with bleeding, pain, or intestinal obstruction. They are identified using characteristic immunohistochemical staining for CD117 and DOG1. Improved understanding of the molecular biology of these tumors and identification of oncogenic drivers have altered the systemic treatment of primarily disseminated disease, which is becoming increasingly complex. Gain-of-function mutations in KIT or PDGFRA genes represent the driving mutations in more than 90% of all GISTs. These patients exhibit good responses to targeted therapy with tyrosine kinase inhibitors (TKIs). Gastrointestinal stromal tumors lacking the KIT/PDGFRA mutations, however, represent distinct clinico-pathological entities with diverse molecular mechanisms of oncogenesis. In these patients, therapy with TKIs is hardly ever as effective as for KIT/PDGFRA-mutated GISTs. This review provides an outline of current diagnostics aimed at identifying clinically relevant driver alterations and a comprehensive summary of current treatments with targeted therapies for patients with GISTs in both adjuvant and metastatic settings. The role of molecular testing and the selection of the optimal targeted therapy according to the identified oncogenic driver are reviewed and some future directions are proposed.
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Tu H, Han Y, Wang Z, Li J. Clustered tree regression to learn protein energy change with mutated amino acid. Brief Bioinform 2022; 23:6702668. [PMID: 36124753 DOI: 10.1093/bib/bbac374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 12/14/2022] Open
Abstract
Accurate and effective prediction of mutation-induced protein energy change remains a great challenge and of great interest in computational biology. However, high resource consumption and insufficient structural information of proteins severely limit the experimental techniques and structure-based prediction methods. Here, we design a structure-independent protocol to accurately and effectively predict the mutation-induced protein folding free energy change with only sequence, physicochemical and evolutionary features. The proposed clustered tree regression protocol is capable of effectively exploiting the inherent data patterns by integrating unsupervised feature clustering by K-means and supervised tree regression using XGBoost, and thus enabling fast and accurate protein predictions with different mutations, with an average Pearson correlation coefficient of 0.83 and an average root-mean-square error of 0.94kcal/mol. The proposed sequence-based method not only eliminates the dependence on protein structures, but also has potential applications in protein predictions with rare structural information.
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Affiliation(s)
- Hongwei Tu
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanqiang Han
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhilong Wang
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinjin Li
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
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Li J, Guo S, Sun Z, Fu Y. Noncoding RNAs in Drug Resistance of Gastrointestinal Stromal Tumor. Front Cell Dev Biol 2022; 10:808591. [PMID: 35174150 PMCID: PMC8841737 DOI: 10.3389/fcell.2022.808591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor in the gastrointestinal tracts and a model for the targeted therapy of solid tumors because of the oncogenic driver mutations in KIT and PDGDRA genes, which could be effectively inhibited by the very first targeted agent, imatinib mesylate. Most of the GIST patients could benefit a lot from the targeted treatment of this receptor tyrosine kinase inhibitor. However, more than 50% of the patients developed resistance within 2 years after imatinib administration, limiting the long-term effect of imatinib. Noncoding RNAs (ncRNAs), the non-protein coding transcripts of human, were demonstrated to play pivotal roles in the resistance of various chemotherapy drugs. In this review, we summarized the mechanisms of how ncRNAs functioning on the drug resistance in GIST. During the drug resistance of GIST, there were five regulating mechanisms where the functions of ncRNAs concentrated: oxidative phosphorylation, autophagy, apoptosis, drug target changes, and some signaling pathways. Also, these effects of ncRNAs in drug resistance were divided into two aspects. How ncRNAs regulate drug resistance in GIST was further summarized according to ncRNA types, different drugs and categories of resistance. Moreover, clinical applications of these ncRNAs in GIST chemotherapies concentrated on the prognostic biomarkers and novel therapeutic targets.
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Affiliation(s)
- Jiehan Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuning Guo
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yang Fu, ; Zhenqiang Sun,
| | - Yang Fu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, China
- *Correspondence: Yang Fu, ; Zhenqiang Sun,
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Xu K, Zhang Q, Chen M, Li B, Wang N, Li C, Gao Z, Zhang D, Yang L, Xu Z, Li X, Xu H. N 6-methyladenosine modification regulates imatinib resistance of gastrointestinal stromal tumor by enhancing the expression of multidrug transporter MRP1. Cancer Lett 2022; 530:85-99. [PMID: 35032557 DOI: 10.1016/j.canlet.2022.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/23/2021] [Accepted: 01/08/2022] [Indexed: 12/29/2022]
Abstract
N6-methyladenosine (m6A) is a frequently occurring mRNA modification, which regulates mRNA stability, splicing, and translation. However, its role in drug resistance of gastrointestinal stromal tumor (GIST) is not known. Here, we report that m6A modification levels are elevated in imatinib-resistant GIST cells and tissues, and that methyltransferase METTL3 is one of the main protein responsible for this aberrant modification. Increased METTL3 levels contributed to imatinib resistance and worse progression-free survival of GIST patients. Mechanistic studies revealed that METTL3-mediated m6A modification of the 5'UTR of the multidrug transporter MRP1 mRNA promoted drug resistance of GIST by stimulating MRP1 mRNA translation, via binding with YTHDF1 and eEF-1. Further, METTL3 transcription in Imatinib resistant GIST cells was activated by ETV1, leading to the increased m6A methylation of MRP1 mRNA. This is the first report showing a novel regulatory mechanism whereby ETV1, METTL3, and the YTHDF1/eEF-1 complex mediate the translation of MRP1 mRNA in an m6A-dependent manner to regulate the intracellular concentration of imatinib and drug resistance of GIST. These findings highlight MRP1 as a new potential therapeutic target for imatinib resistance of GIST.
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Affiliation(s)
- Kangjing Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Qiang Zhang
- Department of Gastrointestinal Surgery, The Second People's Hospital of Lianyungang Affiliated to Kangda College, Nanjing Medical University, Lianyungang, 222002, China
| | - Ming Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Bowen Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Nuofan Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Chao Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Zhishuang Gao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Diancai Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Li Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Xueming Li
- School of Pharmaceutical Science, Nanjing Tech University, Nanjing, 211816, China.
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China.
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Laurini E, Marson D, Aulic S, Fermeglia A, Pricl S. Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Sci Rep 2021; 11:20274. [PMID: 34642465 PMCID: PMC8511038 DOI: 10.1038/s41598-021-99827-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022] Open
Abstract
The purpose of this work is to provide an in silico molecular rationale of the role eventually played by currently circulating mutations in the receptor binding domain of the SARS-CoV-2 spike protein (S-RBDCoV‑2) in evading the immune surveillance effects elicited by the two Eli Lilly LY-CoV555/bamlanivimab and LY-CoV016/etesevimab monoclonal antibodies. The main findings from this study show that, compared to the wild-type SARS-CoV-2 spike protein, mutations E484A/G/K/Q/R/V, Q493K/L/R, S494A/P/R, L452R and F490S are predicted to be markedly resistant to neutralization by LY-CoV555, while mutations K417E/N/T, D420A/G/N, N460I/K/S/T, T415P, and Y489C/S are predicted to confer LY-CoV016 escaping advantage to the viral protein. A challenge of our global in silico results against relevant experimental data resulted in an overall 90% agreement. Thus, the results presented provide a molecular-based rationale for all relative experimental findings, constitute a fast and reliable tool for identifying and prioritizing all present and newly reported circulating spike SARS-CoV-2 variants with respect to antibody neutralization, and yield substantial structural information for the development of next-generation vaccines and monoclonal antibodies more resilient to viral evolution.
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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
| | - Alice 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.
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Gupta A, Singh J, García-Valverde A, Serrano C, Flynn DL, Smith BD. Ripretinib and MEK Inhibitors Synergize to Induce Apoptosis in Preclinical Models of GIST and Systemic Mastocytosis. Mol Cancer Ther 2021; 20:1234-1245. [PMID: 33947686 DOI: 10.1158/1535-7163.mct-20-0824] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/10/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022]
Abstract
The majority of gastrointestinal stromal tumors (GIST) harbor constitutively activating mutations in KIT tyrosine kinase. Imatinib, sunitinib, and regorafenib are available as first-, second-, and third-line targeted therapies, respectively, for metastatic or unresectable KIT-driven GIST. Treatment of patients with GIST with KIT kinase inhibitors generally leads to a partial response or stable disease but most patients eventually progress by developing secondary resistance mutations in KIT. Tumor heterogeneity for secondary resistant KIT mutations within the same patient adds further complexity to GIST treatment. Several other mechanisms converge and reactivate the MAPK pathway upon KIT/PDGFRA-targeted inhibition, generating treatment adaptation and impairing cytotoxicity. To address the multiple potential pathways of drug resistance in GIST, the KIT/PDGFRA inhibitor ripretinib was combined with MEK inhibitors in cell lines and mouse models. Ripretinib potently inhibits a broad spectrum of primary and drug-resistant KIT/PDGFRA mutants and is approved by the FDA for the treatment of adult patients with advanced GIST who have received previous treatment with 3 or more kinase inhibitors, including imatinib. Here we show that ripretinib treatment in combination with MEK inhibitors is effective at inducing and enhancing the apoptotic response and preventing growth of resistant colonies in both imatinib-sensitive and -resistant GIST cell lines, even after long-term removal of drugs. The effect was also observed in systemic mastocytosis (SM) cells, wherein the primary drug-resistant KIT D816V is the driver mutation. Our results show that the combination of KIT and MEK inhibition has the potential to induce cytocidal responses in GIST and SM cells.
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Affiliation(s)
- Anu Gupta
- Deciphera Pharmaceuticals, LLC, Waltham, Massachusetts
| | - Jarnail Singh
- Deciphera Pharmaceuticals, LLC, Waltham, Massachusetts
| | - Alfonso García-Valverde
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - César Serrano
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Bryan D Smith
- Deciphera Pharmaceuticals, LLC, Waltham, Massachusetts.
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Laurini E, Marson D, Aulic S, Fermeglia A, Pricl S. Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. ACS NANO 2021; 15:6929-6948. [PMID: 33733740 PMCID: PMC8009103 DOI: 10.1021/acsnano.0c10833] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The coronavirus disease-2019 (COVID-19) pandemic, caused by the pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), started in China during late 2019 and swiftly spread worldwide. Since COVID-19 emergence, many therapeutic regimens have been relentlessly explored, and although two vaccines have just received emergency use authorization by different governmental agencies, antiviral therapeutics based neutralizing antibodies and small-drug inhibitors can still be vital viable options to prevent and treat SARS-CoV-2 infections. The viral spike glycoprotein (S-protein) is the key molecular player that promotes human host cellular invasion via recognition of and binding to the angiotensin-converting enzyme 2 gene (ACE2). In this work, we report the results obtained by mutating in silico the 18 ACE2 residues and the 14 S-protein receptor binding domain (S-RBDCoV-2) residues that contribute to the receptor/viral protein binding interface. Specifically, each wild-type protein-protein interface residue was replaced by a hydrophobic (isoleucine), polar (serine and threonine), charged (aspartic acid/glutamic acid and lysine/arginine), and bulky (tryptophan) residue, respectively, in order to study the different effects exerted by nature, shape, and dimensions of the mutant amino acids on the structure and strength of the resulting binding interface. The computational results were next validated a posteriori against the corresponding experimental data, yielding an overall agreement of 92%. Interestingly, a non-negligible number of mis-sense variations were predicted to enhance ACE2/S-RBDCoV-2 binding, including the variants Q24T, T27D/K/W, D30E, H34S7T/K, E35D, Q42K, L79I/W, R357K, and R393K on ACE2 and L455D/W, F456K/W, Q493K, N501T, and Y505W on S-RBDCoV-2, respectively.
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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
| | - Alice 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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Abstract
Gastrointestinal stromal tumours (GIST) have an incidence of ~1.2 per 105 individuals per year in most countries. Around 80% of GIST have varying molecular changes, predominantly mutually exclusive activating KIT or PDGFRA mutations, but other, rare subtypes also exist. Localized GIST are curable, and surgery is their standard treatment. Risk factors for relapse are tumour size, mitotic index, non-gastric site and tumour rupture. Patients with GIST with KIT or PDGFRA mutations sensitive to the tyrosine kinase inhibitor (TKI) imatinib that are at high risk of relapse have improved survival with adjuvant imatinib treatment. In advanced disease, median overall survival has improved from 18 months to >70 months since the introduction of TKIs. The role of surgery in the advanced setting remains unclear. Resistance to TKIs arise mainly from subclonal selection of cells with resistance mutations in KIT or PDGFRA when they are the primary drivers. Advanced resistant GIST respond to second-line sunitinib and third-line regorafenib, as well as to the new broad-spectrum TKI ripretinib. Rare molecular forms of GIST with alterations involving NF1, SDH genes, BRAF or NTRK genes generally show primary resistance to standard TKIs, but some respond to specific inhibitors of the activated genes. Despite major advances, many questions in both advanced and localized disease remain unanswered.
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Affiliation(s)
- Jean-Yves Blay
- Department of Medicine, Centre Leon Berard, UNICANCER & University Lyon I, Lyon, France.
| | - Yoon-Koo Kang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Toshiroo Nishida
- Surgery Department, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
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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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11
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Xu K, He Z, Chen M, Wang N, Zhang D, Yang L, Xu Z, Xu H. HIF-1α regulates cellular metabolism, and Imatinib resistance by targeting phosphogluconate dehydrogenase in gastrointestinal stromal tumors. Cell Death Dis 2020; 11:586. [PMID: 32719331 PMCID: PMC7385157 DOI: 10.1038/s41419-020-02768-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
The pentose phosphate pathway (PPP) plays a critical role in maintaining cellular redox homeostasis in tumor cells and macromolecule biosynthesis. Upregulation of the PPP has been shown in several types of tumor. However, how the PPP is regulated to confer selective growth advantages on drug resistant tumor cells is not well understood. Here we show a metabolic shift from tricarboxylic acid cycle (TCA) to PPP after a long period induction of Imatinib (IM). One of the rate-limiting enzymes of the PPP-phosphogluconate dehydrogenase (PGD), is dramatically upregulated in gastrointestinal stromal tumors (GISTs) and GIST cell lines resistant to Imatinib (IM) compared with sensitive controls. Functional studies revealed that the overexpression of PGD in resistant GIST cell lines promoted cell proliferation and suppressed cell apoptosis. Mechanistic analyses suggested that the protein level of hypoxia inducible factor-1α (HIF-1α) increased during long time stimulation of reactive oxygen species (ROS) produced by IM. Importantly, we further demonstrated that HIF-1α also had positive correlation with PGD, resulting in the change of metabolic pathway, and ultimately causing drug resistance in GIST. Our findings show that long term use of IM alters the metabolic phenotype of GIST through ROS and HIF-1α, and this may contribute to IM resistance. Our work offers preclinical proof of metabolic target as an effective strategy for the treatment of drug resistance in GIST.
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Affiliation(s)
- Kangjing Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Zhongyuan He
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Ming Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Nuofan Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Diancai Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Li Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China.
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University, Nanjing, 211166, China.
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12
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Nishida T, Doi T. A new approach to refractory gastrointestinal stromal tumours with diverse acquired mutations. Lancet Oncol 2020; 21:864-865. [PMID: 32511982 DOI: 10.1016/s1470-2045(20)30209-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 10/24/2022]
Affiliation(s)
- Toshirou Nishida
- Department of Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan.
| | - Toshihiko Doi
- Department of Experimental Therapeutics, National Cancer Center Hospital East, Chiba, Japan
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13
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Abstract
Imatinib has revolutionized the treatment of GIST since this drug is able to inhibit tumoral growth by blocking the activity of receptor tyrosine kinases, KIT or PDGFRA, that in these tumors are constitutively activated because of the presence of mutations that alters their catalytic activity. However, despite this enormous improvement in the RFS and OS and in the quality of life of GIST patients, imatinib is not able to eradicate the disease: recurrences occur and acquired resistance is a common event which develops during targeted treatments. Several mechanisms have been demonstrated to be responsible for tumoral growth reactivation which is due to the reactivation of the altered KIT/PDGFRA receptors, no more blocked by the drug. Secondary point mutations are generally observed in the regrowing tumors, and it has been demonstrated that they alter the architectural structure of the site in which the interaction between the drug and the receptor happens. Other mechanisms causing drug resistance have been investigated, indicating that many aspects need to be still explicated and fully understood in order to define a strategy able to fight definitively GIST growth.
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14
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Piras S, Sanna G, Carta A, Corona P, Ibba R, Loddo R, Madeddu S, Caria P, Aulic S, Laurini E, Fermeglia M, Pricl S. Dichloro-Phenyl-Benzotriazoles: A New Selective Class of Human Respiratory Syncytial Virus Entry Inhibitors. Front Chem 2019; 7:247. [PMID: 31041309 PMCID: PMC6476926 DOI: 10.3389/fchem.2019.00247] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/27/2019] [Indexed: 12/14/2022] Open
Abstract
Human Respiratory Syncytial Virus (RSV) is the primary cause of bronchopneumonia in infants and children worldwide. Clinical studies have shown that early treatments of RSV patients with ribavirin improve prognosis, even if the use of this drug is limited due to myelosuppression and toxicity effects. Furthermore, effective vaccines to prevent RSV infection are currently unavailable. Thus, the development of highly effective and specific antiviral drugs for pre-exposure prophylaxis and/or treatment of RSV infections is a compelling need. In the quest of new RSV inhibitors, in this work we evaluated the antiviral activity of a series of variously substituted 5,6-dichloro-1-phenyl-1(2)H-benzo[d][1,2,3]triazole derivatives in cell-based assays. Several 1- and 2-phenyl-benzotriazoles resulted fairly potent (μM concentrations) inhibitors of RSV infection in plaque reduction assays, accompanied by low cytotoxicity in human highly dividing T lymphoid-derived cells and primary cell lines. Contextually, no inhibitory effects were observed against other RNA or DNA viruses assayed, suggesting specific activity against RSV. Further results revealed that the lead compound 10d was active during the early phase of the RSV infection cycle. To understand whether 10d interfered with virus attachment to target cells or virus-cell fusion events, inhibitory activity tests against the RSV mutant strain B1 cp-52—expressing only the F envelope glycoprotein—and a plasmid-based reporter assay that quantifies the bioactivity of viral entry were also performed. The overall biological results, in conjunction with in silico modeling studies, supported the conclusion that the RSV fusion process could be the target of this new series of compounds.
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Affiliation(s)
- Sandra Piras
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Antonio Carta
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - Paola Corona
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - Roberta Ibba
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - Roberta Loddo
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Silvia Madeddu
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Paola Caria
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@Units), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@Units), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@Units), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@Units), DEA, University of Trieste, Trieste, Italy
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15
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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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16
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Zhang Q, Li Z, Xu K, Qian Y, Chen M, Sun L, Song S, Huang X, He Z, Li F, Zhang D, Yang L, Wang Y, Xu H, Xu Z. Intracellular concentration and transporters in imatinib resistance of gastrointestinal stromal tumor. Scand J Gastroenterol 2019; 54:220-226. [PMID: 30879345 DOI: 10.1080/00365521.2019.1577488] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND We aimed to investigate the role of intracellular imatinib concentration in drug resistance and the expression of candidate drug transporters in gastrointestinal stromal tumor (GIST) cell lines. METHOD The imatinib concentrations were measured by the liquid chromatography-tandem mass spectrometry (LC-MS/MS). The expression of candida te drug transporters was detected by qRT-PCR. RESULTS The tissue imatinib concentrations in imatinib resistant patients were significantly lower than that of sensitive patients (p < .05). Compared with parental cell lines, the intracellular imatinib concentration was notably lower in imatinib resistant GIST cell lines. For candidate transporters, MRP1 and BCRP were overexpressed in resistant GIST cell lines. CONCLUSION The intracellular imatinib concentration may play a crucial role in imatinib resistance and the intracellular differences of imatinib concentration may be induced by the upregulation of efflux transporters. Our study highlights the importance of intracellular imatinib concentration and the potential of using imatinib transporters as therapeutic targets for patients with GIST.
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Affiliation(s)
- Qiang Zhang
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Zheng Li
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Kangjing Xu
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Yi Qian
- c Research Division of Clinical Pharmacology , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China
| | - Ming Chen
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Luning Sun
- c Research Division of Clinical Pharmacology , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China
| | - Shanshan Song
- d Department of Pathology , Xuzhou Medical University Affiliated Hospital of Lianyungang , Lianyungang , China
| | - Xiaoxu Huang
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,e Department of Gastrointestinal Surgery , The First Affiliated Yijishan Hospital of Wannan Medical College , Anhui , Wuhu , China
| | - Zhongyuan He
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Fengyuan Li
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Diancai Zhang
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Li Yang
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Yongqing Wang
- c Research Division of Clinical Pharmacology , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China
| | - Hao Xu
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
| | - Zekuan Xu
- a Department of General Surgery , The First Affiliated Hospital of Nanjing Medical University , Nanjing , China.,b Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment , Jiangsu Collaborative Innovation Center for Cancer Personalized Medical University , Nanjing , China
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17
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Wu FX, Wang F, Yang JF, Jiang W, Wang MY, Jia CY, Hao GF, Yang GF. AIMMS suite: a web server dedicated for prediction of drug resistance on protein mutation. Brief Bioinform 2018; 21:318-328. [PMID: 30496338 DOI: 10.1093/bib/bby113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022] Open
Abstract
Drug resistance is one of the most intractable issues for successful treatment in current clinical practice. Although many mutations contributing to drug resistance have been identified, the relationship between the mutations and the related pharmacological profile of drug candidates has yet to be fully elucidated, which is valuable both for the molecular dissection of drug resistance mechanisms and for suggestion of promising treatment strategies to counter resistant. Hence, effective prediction approach for estimating the sensitivity of mutations to agents is a new opportunity that counters drug resistance and creates a high interest in pharmaceutical research. However, this task is always hampered by limited known resistance training samples and accurately estimation of binding affinity. Upon this challenge, we successfully developed Auto In Silico Macromolecular Mutation Scanning (AIMMS), a web server for computer-aided de novo drug resistance prediction for any ligand-protein systems. AIMMS can qualitatively estimate the free energy consequences of any mutations through a fast mutagenesis scanning calculation based on a single molecular dynamics trajectory, which is differentiated with other web services by a statistical learning system. AIMMS suite is available at http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/.
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Affiliation(s)
- Feng-Xu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China
| | - Wen Jiang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China
| | - Meng-Yao Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China
| | - Chen-Yang Jia
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P.R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, P.R. China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, P.R. China
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18
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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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19
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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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20
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Kim WK, Yun S, Park CK, Bauer S, Kim J, Lee MG, Kim H. Sustained Mutant KIT Activation in the Golgi Complex Is Mediated by PKC-θ in Gastrointestinal Stromal Tumors. Clin Cancer Res 2016; 23:845-856. [PMID: 27440273 DOI: 10.1158/1078-0432.ccr-16-0521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/18/2016] [Accepted: 07/11/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE Tumorigenesis of gastrointestinal stromal tumors (GIST) is driven by gain-of-function mutations in the KIT gene, which result in overexpression of activated mutant KIT proteins (MT-KIT). However, the mechanism of MT-KIT overexpression is poorly understood. EXPERIMENTAL DESIGN By protein expression analysis and immunofluorescent microscopic analysis, we determine the stability and localization of MT-KIT in four GIST cell lines with different mutations and HeLa cells transfected with mutant KIT model vectors. We also used 154 human GIST tissues to analyze the relationship between the expression of PKC-θ and MT-KITs, and correlations between PKC-θ overexpression and clinicopathological parameters. RESULTS We report that four different MT-KIT proteins are intrinsically less stable than wild-type KIT due to proteasome-mediated degradation and abnormally localized to the endoplasmic reticulum (ER) or the Golgi complex. By screening a MT-KIT-stabilizing factor, we find that PKC-θ is strongly and exclusively expressed in GISTs and interacts with intracellular MT-KIT to promote its stabilization by increased retention in the Golgi complex. In addition, Western blotting analysis using 50 GIST samples shows strong correlation between PKC-θ and MT-KIT expression (correlation coefficient = 0.682, P < 0.000001). Immunohistochemical analysis using 154 GISTs further demonstrates that PKC-θ overexpression significantly correlates with several clinicopathological parameters such as high tumor grade, frequent recurrence/metastasis, and poor patient survival. CONCLUSIONS Our findings suggest that sustained MT-KIT overexpression through PKC-θ-mediated stabilization in the Golgi contributes to GIST progression and provides a rationale for anti-PKC-θ therapy in GISTs. Clin Cancer Res; 23(3); 845-56. ©2016 AACR.
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Affiliation(s)
- Won Kyu Kim
- Department of Pathology and Brain Korea 21 PLUS Projects for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - SeongJu Yun
- Department of Pathology and Brain Korea 21 PLUS Projects for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Cheol Keun Park
- Department of Pathology and Brain Korea 21 PLUS Projects for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sebastian Bauer
- Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jiyoon Kim
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Goo Lee
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hoguen Kim
- Department of Pathology and Brain Korea 21 PLUS Projects for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea.
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21
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Rusakiewicz S, Perier A, Semeraro M, Pitt JM, Pogge von Strandmann E, Reiners KS, Aspeslagh S, Pipéroglou C, Vély F, Ivagnes A, Jegou S, Halama N, Chaigneau L, Validire P, Christidis C, Perniceni T, Landi B, Berger A, Isambert N, Domont J, Bonvalot S, Terrier P, Adam J, Coindre JM, Emile JF, Poirier-Colame V, Chaba K, Rocha B, Caignard A, Toubert A, Enot D, Koch J, Marabelle A, Lambert M, Caillat-Zucman S, Leyvraz S, Auclair C, Vivier E, Eggermont A, Borg C, Blay JY, Le Cesne A, Mir O, Zitvogel L. NKp30 isoforms and NKp30 ligands are predictive biomarkers of response to imatinib mesylate in metastatic GIST patients. Oncoimmunology 2016; 6:e1137418. [PMID: 28197361 DOI: 10.1080/2162402x.2015.1137418] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/21/2015] [Accepted: 12/28/2015] [Indexed: 12/31/2022] Open
Abstract
Despite effective targeted therapy acting on KIT and PDGFRA tyrosine kinases, gastrointestinal stromal tumors (GIST) escape treatment by acquiring mutations conveying resistance to imatinib mesylate (IM). Following the identification of NKp30-based immunosurveillance of GIST and the off-target effects of IM on NK cell functions, we investigated the predictive value of NKp30 isoforms and NKp30 soluble ligands in blood for the clinical response to IM. The relative expression and the proportions of NKp30 isoforms markedly impacted both event-free and overall survival, in two independent cohorts of metastatic GIST. Phenotypes based on disbalanced NKp30B/NKp30C ratio (ΔBClow) and low expression levels of NKp30A were identified in one third of patients with dismal prognosis across molecular subtypes. This ΔBClow blood phenotype was associated with a pro-inflammatory and immunosuppressive tumor microenvironment. In addition, detectable levels of the NKp30 ligand sB7-H6 predicted a worse prognosis in metastatic GIST. Soluble BAG6, an alternate ligand for NKp30 was associated with low NKp30 transcription and had additional predictive value in GIST patients with high NKp30 expression. Such GIST microenvironments could be rescued by therapy based on rIFN-α and anti-TRAIL mAb which reinstated innate immunity.
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Affiliation(s)
- Sylvie Rusakiewicz
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Villejuif, France
| | - Aurélie Perier
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France
| | - Michaela Semeraro
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France; Department of Pediatric Oncology, GRCC, Villejuif, France
| | - Jonathan M Pitt
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France
| | | | - Katrin S Reiners
- Department of Internal Medicine I, University Hospital of Cologne , Cologne, Germany
| | - Sandrine Aspeslagh
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France; Drug Development Department (DITEP), GRCC, Villejuif, France
| | - Christelle Pipéroglou
- Hôpital de la Conception, Assistance Publique-Hôpitaux de Marseille , Marseille, France
| | - Frédéric Vély
- Hôpital de la Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France; INSERM, U1104, Centre d'Immunologie de Marseille-Luminy, Marseille, France; CNRS, UMR7280, Marseille, France
| | - Alexandre Ivagnes
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France
| | - Sarah Jegou
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France
| | - Niels Halama
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg, Germany; National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Loic Chaigneau
- Department of Medical Oncology, Centre Hospitalier Universitaire Jean Minjoz , Besançon, France
| | - Pierre Validire
- Department of Pathology, Institut Mutualiste Montsouris, Paris, France; Department of Medical Oncology, Sarcoma, Institut Mutualiste Montsouris, Paris, France
| | - Christos Christidis
- Department of Medical Oncology, Sarcoma, Institut Mutualiste Montsouris, Paris, France; Department of Surgery, Institut Mutualiste Montsouris, University of Paris Descartes 5, Paris, France
| | - Thierry Perniceni
- Department of Medical Oncology, Sarcoma, Institut Mutualiste Montsouris , Paris, France
| | - Bruno Landi
- Department of Gastroenterology and Digestive Oncology, Georges Pompidou European Hospital, University of Paris Descartes 5 , Paris, France
| | - Anne Berger
- Department of Surgery, Georges Pompidou European Hospital, University of Paris Descartes , Paris, France
| | - Nicolas Isambert
- Department of Medical Oncology, Centre Georges-François Leclerc , Dijon, France
| | - Julien Domont
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Department of Medicine, Sarcoma committee, GRCC, Villejuif, France
| | - Sylvie Bonvalot
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Department of Medicine, Sarcoma committee, GRCC, Villejuif, France; Department of Surgery, GRCC, Villejuif, France
| | - Philippe Terrier
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Department of Medicine, Sarcoma committee, GRCC, Villejuif, France; Department of Pathology, GRCC, Villejuif, France; Center of Biological Resources, GRCC, Villejuif, France
| | - Julien Adam
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Department of Pathology, GRCC, Villejuif, France; Center of Biological Resources, GRCC, Villejuif, France
| | | | | | - Vichnou Poirier-Colame
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France
| | - Kariman Chaba
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France; INSERM, U1138, Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
| | - Benedita Rocha
- INSERM, U1020, Paris, France; Faculté de Médecine René Descartes, Paris, France
| | - Anne Caignard
- INSERM, U1160, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Groupe Hospitalier Saint Louis-Lariboisière - F. Vidal, Paris, France
| | - Antoine Toubert
- INSERM, U1160, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Groupe Hospitalier Saint Louis-Lariboisière - F. Vidal, Paris, France
| | - David Enot
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France; INSERM, U1138, Paris, France; Metabolomics and Cell Biology platforms, GRCC, Villejuif, France
| | - Joachim Koch
- Institute of Medical Microbiology and Hygiene, University of Mainz Medical Centre , Mainz, Germany
| | - Aurélien Marabelle
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France; Drug Development Department (DITEP), GRCC, Villejuif, France
| | - Marion Lambert
- INSERM, U1149, Equipe "Immunité innée chez l'enfant", Hôpital Robert Debré , Paris, France
| | - Sophie Caillat-Zucman
- INSERM, U1149, Equipe "Immunité innée chez l'enfant", Hôpital Robert Debré , Paris, France
| | - Serge Leyvraz
- Department of Oncology, University Hospital , Lausanne, Switzerland
| | - Christian Auclair
- Applied Biology and Pharmacology Laboratory, Ecole Normale Supèrieur of Cachan , Cachan, France
| | - Eric Vivier
- INSERM, U1104, Centre d'Immunologie de Marseille-Luminy, Marseille, France; CNRS, UMR7280, Marseille, France; Aix Marseille Université, UM2, Marseille, France
| | | | | | - Jean-Yves Blay
- Department of Medicine, Centre Léon Bérard & Université Claude Bernard Lyon I, DGOS-INCA SIRIC , Lyon, France
| | - Axel Le Cesne
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Department of Medicine, Sarcoma committee, GRCC, Villejuif, France
| | - Olivier Mir
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; Department of Medicine, Sarcoma committee, GRCC, Villejuif, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France; INSERM, U1015, IGR, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Villejuif, France; University of Paris Sud XI, Villejuif, France
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22
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Beiranvand Z, Bani F, Kakanejadifard A, Laurini E, Fermeglia M, Pricl S, Adeli M. Anticancer drug delivery systems based on specific interactions between albumin and polyglycerol. RSC Adv 2016. [DOI: 10.1039/c5ra25463a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Since albumin is the main transporter and the most abundant protein in the blood, interactions between this protein and drug/gene nanocarriers are of great importance to ensure successful delivery to target tissue(s) in the body.
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Affiliation(s)
- Zahra Beiranvand
- Faculty of Science
- Department of Chemistry
- Lorestan University
- Khorramabad
- Iran
| | - Farhad Bani
- Institue of Biochemistry and Biophysic
- University of Tehran
- Iran
| | - Ali Kakanejadifard
- Faculty of Science
- Department of Chemistry
- Lorestan University
- Khorramabad
- Iran
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory
- DEA
- University of Trieste
- 34127 Trieste
- Italy
| | - Maurizio Fermeglia
- Molecular Simulation Engineering (MOSE) Laboratory
- DEA
- University of Trieste
- 34127 Trieste
- Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory
- DEA
- University of Trieste
- 34127 Trieste
- Italy
| | - Mohsen Adeli
- Faculty of Science
- Department of Chemistry
- Lorestan University
- Khorramabad
- Iran
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23
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Briguglio I, Loddo R, Laurini E, Fermeglia M, Piras S, Corona P, Giunchedi P, Gavini E, Sanna G, Giliberti G, Ibba C, Farci P, La Colla P, Pricl S, Carta A. Synthesis, cytotoxicity and antiviral evaluation of new series of imidazo[4,5-g]quinoline and pyrido[2,3-g]quinoxalinone derivatives. Eur J Med Chem 2015; 105:63-79. [DOI: 10.1016/j.ejmech.2015.10.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 10/23/2022]
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24
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Wang Y, Liu X, Laurini E, Posocco P, Ziarelli F, Fermeglia M, Qu F, Pricl S, Zhang CC, Peng L. Mimicking the 2-oxoglutaric acid signalling function using molecular probes: insights from structural and functional investigations. Org Biomol Chem 2015; 12:4723-9. [PMID: 24869624 DOI: 10.1039/c4ob00630e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
2-Oxoglutaric acid (2-OG) has gained considerable attention because of its newly discovered signalling role in addition to its established metabolic functions. With the aim of further exploring the signalling function of 2-OG, here we present a structure-activity relationship study using 2-OG probes bearing different carbon chain lengths and terminal groups. Our results highlight the importance of the five-membered carbon molecular skeleton and of the two carboxylic terminals in maintaining the signalling functions of the parent molecule 2-OG. These findings provide valuable information for designing new, effective molecular probes able to dissect and discriminate the newly discovered, complex signalling role of 2-OG from its canonical activity in metabolism.
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Affiliation(s)
- Yang Wang
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288, Marseille, France.
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25
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Mehta VR, Khan U, Hoang U, Rachshtut M. Killing two birds with one stone: a case of GIST and supervening CML. BMJ Case Rep 2015; 2015:bcr-2015-211698. [PMID: 26468222 DOI: 10.1136/bcr-2015-211698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A 50-year-old patient who presented with abdominal pain was found to have a suspicious 8 × 6 × 9 cm mass in the left upper abdomen on imaging. A complete surgical resection of the mass was performed subsequently and pathology revealed a gastrointestinal stromal tumour. The patient was started on adjuvant Imatinib following the resection. Four years later, reimaging demonstrated no evidence of disease and adjuvant therapy was discontinued. Nine months following discontinuation of Imatinib, routine blood work revealed marked leucocytosis. Further work up including peripheral smear and bone marrow biopsy showed findings consistent with chronic myelogenous leucaemia. Imatinib was restarted and the patient's white cell counts returned to normal range within a month.
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Affiliation(s)
- Vivek Rashmikant Mehta
- Department of Internal Medicine, Mercy Catholic Medical Center, Darby, Pennsylvania, USA Mercy Catholic Medical Center, Philadelphia, Pennsylvania, USA
| | - Uzma Khan
- Department of Internal Medicine, Mercy Catholic Medical Center, Darby, Pennsylvania, USA
| | - Uyen Hoang
- Sinai Hospital of Baltimore, Baltimore, Maryland, USA
| | - Michael Rachshtut
- Department of Hematology Oncology, Mercy Catholic Medical Center, Philadelphia, Pennsylvania, USA
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26
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27
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Tang HC, Chen YC. Insight into molecular dynamics simulation of BRAF(V600E) and potent novel inhibitors for malignant melanoma. Int J Nanomedicine 2015; 10:3131-46. [PMID: 25960652 PMCID: PMC4412490 DOI: 10.2147/ijn.s80150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BRAF inhibitors have changed the standard therapeutic protocol for advanced or metastatic melanoma which harbored notorious BRAF(V600E) single mutation. However, drug resistance to BRAF inhibitors happens just like other cancer treatment. In this study, we constructed the ideal BRAF(V600E)-modeled structure through homology modeling and introduced the method of structure-based docking or virtual screening from the large compound database. Through certain methods of molecular dynamics simulation, we realized that BRAF(V600E) had quite prominent difference of molecular character or structural variation from the wild-type BRAF protein. It might confer the metamorphic character of advanced melanoma for the patients who harbored BRAF(V600E) mutation. By the methods of ligand-based quantitative structure-activity relationship and molecular dynamics simulation, we further recommend that aknadicine and 16beta-hydroxy-19s-vindolinine N-oxide from the traditional Chinese medicine are potent novel inhibitors for the management of malignant melanoma in the future.
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Affiliation(s)
- Hsin-Chieh Tang
- Department of Biomedical Informatics, Asia University, Taichung, Taiwan
| | - Yu-Chian Chen
- Department of Biomedical Informatics, Asia University, Taichung, Taiwan ; Human Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan ; Research Center for Chinese Medicine and Acupuncture, China Medical University Hospital, Taichung, Taiwan
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28
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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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29
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Carbonell P, Trosset JY. Overcoming drug resistance through in silico prediction. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 11:101-7. [PMID: 24847659 DOI: 10.1016/j.ddtec.2014.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Prediction tools are commonly used in pre-clinical research to assist target selection, to optimize drug potency or to predict the pharmacological profile of drug candidates. In silico prediction and overcoming drug resistance is a new opportunity that creates a high interest in pharmaceutical research. This review presents two main in silico strategies to meet this challenge: a structure-based approach to study the influence of mutations on the drug-target interaction and a system-biology approach to identify resistance pathways for a given drug. In silico screening of synergies between therapeutic and resistant pathways through biological network analysis is an example of technique to escape drug resistance. Structure-based drug design and in silico system biology are complementary approaches to reach few objectives at once: increase efficiency, reduce toxicity and overcoming drug resistance.
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30
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Augmentation of multiple protein kinase activities associated with secondary imatinib resistance in gastrointestinal stromal tumors as revealed by quantitative phosphoproteome analysis. J Proteomics 2014; 115:132-42. [PMID: 25554490 DOI: 10.1016/j.jprot.2014.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/10/2014] [Accepted: 12/16/2014] [Indexed: 11/23/2022]
Abstract
UNLABELLED Mutations in the Kit receptor tyrosine kinase gene (KIT), which result in constitutive activation of the protein (KIT), are causally related to the development of gastrointestinal stromal tumors (GISTs). Imatinib, a targeted anticancer drug, exerts a therapeutic effect against GISTs by repressing the kinase activity of KIT. Long-term administration of this drug, however, causes the emergence of imatinib-resistant GISTs. We performed quantitative phosphoproteome analysis using a cell-based GIST model system comprising an imatinib-sensitive GIST cell line (GIST882), GIST882 under treatment with imatinib (GIST882-IM), and secondary imatinib-resistant GIST882 (GIST882-R). Phosphorylated peptides were purified from each cell line using titania-based affinity chromatography or anti-phosphotyrosine immunoprecipitation, and then subjected to LC-MS/MS based quantitative phosphoproteome analysis. Using this method we identified augmentation of the kinase activities of multiple elements of the signal transduction pathway, especially KIT and EGFR. Although, these elements were up-regulated in GIST882-R, no additionally mutated KIT mRNA was found in secondary imatinib-resistant GIST cells. Treatment of GIST882-R with imatinib in combination with gefitinib, an EGFR inhibitor, partially prevented cell growth, implying that EGFR may be involved in acquisition of secondary imatinib resistance in GIST. BIOLOGICAL SIGNIFICANCE In this study, we performed a quantitative phosphoproteome analysis using a cell culture-based GIST model system. The goal of the study was to investigate the mechanism of acquired resistance in GISTs against imatinib, a molecularly targeted drug that inhibits kinase activity of the KIT protein and that has been approved for the treatment of GISTs. In imatinib-resistant GIST cells, we observed elevated expression of KIT and restoration of its kinase activity, as well as activation of multiple proliferative signaling pathways. Our results indicate that the effects of even so-called 'molecularly targeted' drugs, are broad rather than convergent, and that the mechanisms of action of such drugs during continuous administration are extremely complex.
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31
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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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32
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Rigoni A, Colombo MP, Pucillo C. The Role of Mast Cells in Molding the Tumor Microenvironment. CANCER MICROENVIRONMENT 2014; 8:167-76. [PMID: 25194694 DOI: 10.1007/s12307-014-0152-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 08/20/2014] [Indexed: 12/20/2022]
Abstract
Mast cells (MCs) are granulocytic immune cells that reside in tissues exposed to the external environment. MCs are best known for their activity in allergic reactions, but they have been involved in different physiological and pathological conditions. In particular, MC infiltration has been shown in several types of human tumors and in animal cancer models. Nevertheless, the role of MCs in the tumor microenvironment is still debated because they have been associated either to good or poor prognosis depending on tumor type and tissue localization. This dichotomous role relies on MC capacity to secrete a broad spectrum of molecules with modulatory functions, which may condition the final tumor outcome also promoting angiogenesis and tissue remodeling. In this review, we analyze the multifaceted role of mast cell in tumor progression and inhibition considering their ability to interact with: i) immune cells, ii) tumor cells and iii) the extracellular matrix. Eventually, the current MC targeting strategies to treat cancer patients are discussed. Deciphering the actual role of MCs in tumor onset and progression is crucial to identify MC-targeted treatments aimed at killing cancer cells or at making the tumor vulnerable to selected anti-cancer drugs.
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Affiliation(s)
- A Rigoni
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, via Amadeo 42, 20133, Milan, Italy
| | - M P Colombo
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, via Amadeo 42, 20133, Milan, Italy.
| | - C Pucillo
- Department of Medical and Biological Sciences, University of Udine, 33100, Udine, Italy
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33
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Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy. Proc Natl Acad Sci U S A 2014; 111:3550-5. [PMID: 24550512 DOI: 10.1073/pnas.1321173111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The acquisition of mutations within the BCR-ABL1 kinase domain is frequently associated with tyrosine kinase inhibitor (TKI) failure in chronic myeloid leukemia. Sensitive sequencing techniques have revealed a high prevalence of compound BCR-ABL1 mutations (polymutants) in patients failing TKI therapy. To investigate the molecular consequences of such complex mutant proteins with regards to TKI resistance, we determined by cloning techniques the presence of polymutants in a cohort of chronic-phase patients receiving imatinib followed by dasatinib therapy. The analysis revealed a high frequency of polymutant BCR-ABL1 alleles even after failure of frontline imatinib, and also the progressive exhaustion of the pool of unmutated BCR-ABL1 alleles over the course of sequential TKI therapy. Molecular dynamics analyses of the most frequent polymutants in complex with TKIs revealed the basis of TKI resistance. Modeling of BCR-ABL1 in complex with the potent pan-BCR-ABL1 TKI ponatinib highlighted potentially effective therapeutic strategies for patients carrying these recalcitrant and complex BCR-ABL1 mutant proteins while unveiling unique mechanisms of escape to ponatinib therapy.
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Herrmann MD, Lennerz JK, Bullinger L, Bartholomae S, Holzmann K, Westhoff MA, Corbacioglu S, Debatin KM. Transitory dasatinib-resistant states in KITmut t(8;21) acute myeloid leukemia cells correlate with altered KIT expression. Exp Hematol 2014; 42:90-100. [DOI: 10.1016/j.exphem.2013.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 09/30/2013] [Accepted: 10/23/2013] [Indexed: 11/29/2022]
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Lee EJ, Kang G, Kang SW, Jang KT, Lee J, Park JO, Park CK, Sohn TS, Kim S, Kim KM. GSTT1 copy number gain and ZNF overexpression are predictors of poor response to imatinib in gastrointestinal stromal tumors. PLoS One 2013; 8:e77219. [PMID: 24124608 PMCID: PMC3790698 DOI: 10.1371/journal.pone.0077219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/01/2013] [Indexed: 01/25/2023] Open
Abstract
Oncogenic mutations in gastrointestinal stromal tumors (GISTs) predict prognosis and therapeutic responses to imatinib. In wild-type GISTs, the tumor-initiating events are still unknown, and wild-type GISTs are resistant to imatinib therapy. We performed an association study between copy number alterations (CNAs) identified from array CGH and gene expression analyses results for four wild-type GISTs and an imatinib-resistant PDGFRA D842V mutant GIST, and compared the results to those obtained from 27 GISTs with KIT mutations. All wild-type GISTs had multiple CNAs, and CNAs in 1p and 22q that harbor the SDHB and GSTT1 genes, respectively, correlated well with expression levels of these genes. mRNA expression levels of all SDH gene subunits were significantly lower (P≤0.041), whereas mRNA expression levels of VEGF (P=0.025), IGF1R (P=0.026), and ZNFs (P<0.05) were significantly higher in GISTs with wild-type/PDGFRA D842V mutations than GISTs with KIT mutations. qRT-PCR validation of the GSTT1 results in this cohort and 11 additional malignant GISTs showed a significant increase in the frequency of GSTT1 CN gain and increased mRNA expression of GSTT1 in wild-type/PDGFRA D842V GISTs than KIT-mutant GISTs (P=0.033). Surprisingly, all four malignant GISTs with KIT exon 11 deletion mutations with primary resistance to imatinib had an increased GSTT1 CN and mRNA expression level of GSTT1. Increased mRNA expression of GSTT1 and ZNF could be predictors of a poor response to imatinib. Our integrative approach reveals that for patients with wild-type (or imatinib-resistant) GISTs, attempts to target VEGFRs and IGF1R may be reasonable options.
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Affiliation(s)
- Eui Jin Lee
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Guhyun Kang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Sanggye Paik Hospital, Inje University College of Medicine, Seoul, Korea
| | - Shin Woo Kang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Mathematics, Korea University, Seoul, Korea
| | - Kee-Taek Jang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Oh Park
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Cheol Keun Park
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Sung Sohn
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- * E-mail:
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Comprehensive Analysis of ETS Family Members in Melanoma by Fluorescence In Situ Hybridization Reveals Recurrent ETV1 Amplification. Transl Oncol 2013; 6:405-12. [PMID: 23908683 DOI: 10.1593/tlo.13340] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/02/2013] [Accepted: 05/05/2013] [Indexed: 12/15/2022] Open
Abstract
E26 transformation-specific (ETS) transcription factors are known to be involved in gene aberrations in various malignancies including prostate cancer; however, their role in melanoma oncogenesis has yet to be fully explored. We have completed a comprehensive fluorescence in situ hybridization (FISH)-based screen for all 27 members of the ETS transcription factor family on two melanoma tissue microarrays, representing 223 melanomas, 10 nevi, and 5 normal skin tissues. None of the melanoma cases demonstrated ETS fusions; however, 6 of 114 (5.3%) melanomas were amplified for ETV1 using a break-apart FISH probe. For the six positive cases, locus-controlled FISH probes revealed that two of six cases were amplified for the ETV1 region, whereas four cases showed copy gains of the entire chromosome 7. The remaining 26 ETS family members showed no chromosomal aberrations by FISH. Quantitative polymerase chain reaction showed an average 3.4-fold (P value = .00218) increased expression of ETV1 in melanomas, including the FISH ETV1-amplified cases, when compared to other malignancies (prostate, breast, and bladder carcinomas). These data suggest that a subset of melanomas overexpresses ETV1 and amplification of ETV1 may be one mechanism for achieving high gene expression.
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Linch M, Claus J, Benson C. Update on imatinib for gastrointestinal stromal tumors: duration of treatment. Onco Targets Ther 2013; 6:1011-23. [PMID: 23935374 PMCID: PMC3735340 DOI: 10.2147/ott.s31260] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common sarcoma of the gastrointestinal tract, with transformation typically driven by activating mutations of c-KIT and less commonly platelet-derived growth factor receptor alpha (PDGFRA). Successful targeting of c-KIT and PDGFRA with imatinib, a tyrosine kinase inhibitor (TKI), has had a major impact in advanced GIST and as an adjuvant and neoadjuvant treatment. If treatment with imatinib fails, further lines of TKI therapy have a role, but disease response is usually only measured in months, so strategies to maximize the benefit from imatinib are paramount. Here, we provide an overview of the structure and signaling of c-KIT coupled with a review of the clinical trials of imatinib in GIST. In doing so, we make recommendations about the duration of imatinib therapy and suggest how best to utilize imatinib in order to improve patient outcomes in the future.
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Affiliation(s)
- Mark Linch
- Sarcoma Unit, Royal Marsden Hospital, United Kingdom ; Protein Phosphorylation Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
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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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39
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Laurini E, Posocco P, Fermeglia M, Gibbons DL, Quintás-Cardama A, Pricl S. Through the open door: Preferential binding of dasatinib to the active form of BCR-ABL unveiled by in silico experiments. Mol Oncol 2013; 7:968-75. [PMID: 23816609 DOI: 10.1016/j.molonc.2013.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 11/19/2022] Open
Abstract
Dasatinib is a second-generation BCR-ABL inhibitor approved for the treatment of patients with chronic myeloid leukemia, both in the frontline and in the imatinib-resistant/intolerant settings. The high affinity of dasatinib for the protein is currently assumed to result from its ability to bind both the active and inactive conformations of the BCR-ABL kinase. In the present work, using state of the art molecular simulation techniques we prove that dasatinib exhibits a highly selective preference for the active (open) BCR-ABL conformation. By using three different BCR-ABL conformations (active, inactive, and intermediate inactive) we show that, from a thermodynamic standpoint, the affinity of dasatinib for BCR-ABL drastically decreases in the order: active > alternative inactive > inactive, as a result of differential contributions from the single residues lining the kinase binding pocket and the concomitant stabilization/destabilization of the kinase hydrophobic spine. Molecule-pulling experiments also corroborate this trend as significantly lower forces and smaller times are required to extract dasatinib from its inactive BCR-ABL complexes with respect to the active complex counterparts. Importantly, our results support recent NMR solution results demonstrating no evidence of dasatinib bound to the inactive form of BCR-ABL.
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Affiliation(s)
- Erik Laurini
- Molecular Simulations Engineering (MOSE) Laboratory - DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
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40
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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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41
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Rusakiewicz S, Semeraro M, Sarabi M, Desbois M, Locher C, Mendez R, Vimond N, Concha A, Garrido F, Isambert N, Chaigneau L, Le Brun-Ly V, Dubreuil P, Cremer I, Caignard A, Poirier-Colame V, Chaba K, Flament C, Halama N, Jäger D, Eggermont A, Bonvalot S, Commo F, Terrier P, Opolon P, Emile JF, Coindre JM, Kroemer G, Chaput N, Le Cesne A, Blay JY, Zitvogel L. Immune infiltrates are prognostic factors in localized gastrointestinal stromal tumors. Cancer Res 2013; 73:3499-510. [PMID: 23592754 DOI: 10.1158/0008-5472.can-13-0371] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cancer immunosurveillance relies on effector/memory tumor-infiltrating CD8(+) T cells with a T-helper cell 1 (TH1) profile. Evidence for a natural killer (NK) cell-based control of human malignancies is still largely missing. The KIT tyrosine kinase inhibitor imatinib mesylate markedly prolongs the survival of patients with gastrointestinal stromal tumors (GIST) by direct effects on tumor cells as well as by indirect immunostimulatory effects on T and NK cells. Here, we investigated the prognostic value of tumor-infiltrating lymphocytes (TIL) expressing CD3, Foxp3, or NKp46 (NCR1) in a cohort of patients with localized GIST. We found that CD3(+) TIL were highly activated in GIST and were especially enriched in areas of the tumor that conserve class I MHC expression despite imatinib mesylate treatment. High densities of CD3(+) TIL predicted progression-free survival (PFS) in multivariate analyses. Moreover, GIST were infiltrated by a homogeneous subset of cytokine-secreting CD56(bright) (NCAM1) NK cells that accumulated in tumor foci after imatinib mesylate treatment. The density of the NK infiltrate independently predicted PFS and added prognostic information to the Miettinen score, as well as to the KIT mutational status. NK and T lymphocytes preferentially distributed to distinct areas of tumor sections and probably contributed independently to GIST immunosurveillance. These findings encourage the prospective validation of immune biomarkers for optimal risk stratification of patients with GIST.
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Affiliation(s)
- Sylvie Rusakiewicz
- Institut Gustave Roussy; Institut National de la Santé et de la Recherche Medicale (INSERM) U1015, France
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42
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Amadio M, Pascale A, Govoni S, Laurini E, Pricl S, Gaggeri R, Rossi D, Collina S. Identification of Peptides with ELAV-like mRNA-Stabilizing Effect: An IntegratedIn Vitro/In SilicoApproach. Chem Biol Drug Des 2013; 81:707-14. [DOI: 10.1111/cbdd.12117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/10/2012] [Accepted: 01/29/2013] [Indexed: 01/18/2023]
Affiliation(s)
- Marialaura Amadio
- Pharmacology Section, Department of Drug Sciences; University of Pavia; Viale Taramelli 12; Pavia; 27100; Italy
| | - Alessia Pascale
- Pharmacology Section, Department of Drug Sciences; University of Pavia; Viale Taramelli 12; Pavia; 27100; Italy
| | - Stefano Govoni
- Pharmacology Section, Department of Drug Sciences; University of Pavia; Viale Taramelli 12; Pavia; 27100; Italy
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, Department of Industrial Engineering and Information Technology; University of Trieste; Via A. Valerio 10; Trieste; 34127; Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, Department of Industrial Engineering and Information Technology; University of Trieste; Via A. Valerio 10; Trieste; 34127; Italy
| | - Raffaella Gaggeri
- Medicinal Chemistry and Pharmaceutical Technology Section, Department of Drug Sciences; University of Pavia; Viale Taramelli 12; Pavia; 27100; Italy
| | - Daniela Rossi
- Medicinal Chemistry and Pharmaceutical Technology Section, Department of Drug Sciences; University of Pavia; Viale Taramelli 12; Pavia; 27100; Italy
| | - Simona Collina
- Medicinal Chemistry and Pharmaceutical Technology Section, Department of Drug Sciences; University of Pavia; Viale Taramelli 12; Pavia; 27100; Italy
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43
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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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44
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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: 17] [Impact Index Per Article: 1.5] [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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45
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Abstract
Resistance to drugs that treat infectious disease is a major problem worldwide. The rapid emergence of drug resistance is not well understood. We present two in silico models for the discovery of drug resistance mechanisms and for combating the evolution of resistance, respectively. In the first model, we computationally investigated subgraphs of a biological interaction network that show substantial adaptations when cells transcriptionally respond to a changing environment or treatment. As a case study, we investigated the response of the malaria parasite Plasmodium falciparum to chloroquine and tetracycline treatments. The second model involves a machine learning technique that combines clustering, common distance similarity measurements, and hierarchical clustering to propose new combinations of drug targets.
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Affiliation(s)
- Segun Fatumo
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
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46
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Bourillon A, Hu HH, Hetet G, Lacapere JJ, André J, Descamps V, Basset-Seguin N, Ogbah Z, Puig S, Saiag P, Bagot M, Bensussan A, Grandchamp B, Dumaz N, Soufir N. Genetic variation at KIT locus may predispose to melanoma. Pigment Cell Melanoma Res 2012; 26:88-96. [PMID: 23020152 DOI: 10.1111/pcmr.12032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 09/28/2012] [Indexed: 01/06/2023]
Abstract
As loss of KIT frequently occurs in melanoma progression, we hypothesized that KIT is implicated in predisposition to melanoma (MM). Thus, we sequenced the KIT coding region in 112 familial MM cases and 143 matched controls and genotyped tag single-nucleotide polymorphisms (SNPs) in two cohorts of melanoma patients and matched controls. Five rare KIT substitutions, all predicted possibly or probably deleterious, were identified in five patients, but none in controls [RR = 2.26 (1.26-2.26)]. Expressed in melanocyte lines, three substitutions inhibited KIT signaling. Comparison with exomes database (7020 alleles) confirmed a significant excess of rare deleterious KIT substitutions in patients. Additionally, a common SNP, rs2237028, was associated with MM risk, and 6 KIT variants were associated with nevus count. Our data strongly suggest that rare KIT substitutions predispose to melanoma and that common variants at KIT locus may also impact nevus count and melanoma risk.
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Affiliation(s)
- Agnes Bourillon
- Département de Génétique, Hôpital Bichat-Claude Bernard, APHP, Paris, France
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47
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Du X, Wang QR, Chan E, Merchant M, Liu J, French D, Ashkenazi A, Qing J. FGFR3 stimulates stearoyl CoA desaturase 1 activity to promote bladder tumor growth. Cancer Res 2012; 72:5843-55. [PMID: 23019225 DOI: 10.1158/0008-5472.can-12-1329] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fibroblast growth factor receptor 3 (FGFR3) belongs to a family of receptor tyrosine kinases that control cell proliferation, differentiation, and survival. Aberrant activation of FGFR3 via overexpression or mutation is a frequent feature of bladder cancer; however, its molecular and cellular consequences and functional relevance to carcinogenesis are not well understood. Through transcriptional profiling of bladder carcinoma cells subjected to short hairpin RNA knockdown of FGFR3, we identified a gene-signature linking FGFR3 signaling with de novo sterol and lipid biosynthesis and metabolism. We found that FGFR3 signaling promotes the cleavage and activation of the master transcriptional regulator of lipogenesis, sterol regulatory element-binding protein 1(SREBP1/SREBF1), in a PI3K-mTORC1-dependent fashion. In turn, SREBP1 regulates the expression of key lipogenic enzymes, including stearoyl CoA desaturase 1 (SCD1/SCD). SCD1 is the rate-limiting enzyme in the biosynthesis of monounsaturated fatty acids and is crucial for lipid homeostasis. In human bladder cancer cell lines expressing constitutively active FGFR3, knockdown of SCD1 by siRNA markedly attenuated cell-cycle progression, reduced proliferation, and induced apoptosis. Furthermore, inducible knockdown of SCD1 in a bladder cancer xenograft model substantially inhibited tumor progression. Pharmacologic inhibition of SCD1 blocked fatty acid desaturation and also exerted antitumor activity in vitro and in vivo. Together, these findings reveal a previously unrecognized role of FGFR3 in regulating lipid metabolism to maintain tumor growth and survival, and also identify SCD1 as a potential therapeutic target for FGFR3-driven bladder cancer.
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Affiliation(s)
- Xiangnan Du
- Molecular Oncology, Cancer Signaling and Translational Oncology, Bioinformatics, and Pathology, Genentech, Inc, South San Francisco, California 94080, USA
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48
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Verstraete K, Savvides SN. Extracellular assembly and activation principles of oncogenic class III receptor tyrosine kinases. Nat Rev Cancer 2012; 12:753-66. [PMID: 23076159 DOI: 10.1038/nrc3371] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Intracellular signalling cascades initiated by class III receptor tyrosine kinases (RTK-IIIs) and their cytokine ligands contribute to haematopoiesis and mesenchymal tissue development. They are also implicated in a wide range of inflammatory disorders and cancers. Recent snapshots of RTK-III ectodomains in complex with cognate cytokines have revealed timely insights into the structural determinants of RTK-III activation, evolution and pathology. Importantly, candidate 'driver' and 'passenger' mutations that have been identified in RTK-IIIs can now be collectively mapped for the first time to structural scaffolds of the corresponding RTK-III ectodomains. Such insights will generate a renewed interest in dissecting the mechanistic effects of such mutations and their therapeutic relevance.
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Affiliation(s)
- Kenneth Verstraete
- Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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Minárik G, Plank L, Lasabová Z, Szemes T, Burjanivová T, Szépe P, Buzalková V, Porubský D, Sufliarsky J. Spectrum of mutations in gastrointestinal stromal tumor patients - a population-based study from Slovakia. APMIS 2012; 121:539-48. [PMID: 23106360 DOI: 10.1111/apm.12019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 09/25/2012] [Indexed: 01/23/2023]
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of gastrointestinal tract and are characterized by presence of mutations in tyrosine kinases cKIT (KIT) and PDGFRα (PDGFRA). Mutations identified are highly heterogeneous, but some mutations are associated with specific clinical features of the tumor. Samples from 278 GIST patients collected during the period 2004-2011 were screened for mutations in exons 9, 11, 13, and 17 of KIT and 12, 14 and 18 of PDGFRA. Results of mutation screening were summarized and tested for possible association with clinical parameters of tumors. Mutations were identified in 83.81% of patients. Most frequent mutations were found in KIT exon 11 reaching frequency of 62.95%. Other exons contributed to the mutation pool with frequencies 8.27%, 7.55%, 2.52%, 1.44%, 1.08%, and 0.00%, in decreasing order KIT exon 9, PDGRFA exons 18 and 12, KIT exon 13, PDGFRA exon 14, and KIT exon 17. General linear model analysis showed no effect of any individual analyzed mutation on the phenotypic variables, but we confirmed association between mutations KIT exon 9 p. 503-504_dup2, and PDGFRA exon 18 p. D842V and intestinal and gastric localization of tumors.
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Affiliation(s)
- Gabriel Minárik
- Faculty of Medicine, Institute of Molecular Biomedicine, Comenius University in Bratislava, Bratislava, Slovakia.
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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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