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Martínez-Castillo M, Gómez-Romero L, Tovar H, Olarte-Carrillo I, García-Laguna A, Barranco-Lampón G, De la Cruz-Rosas A, Martínez-Tovar A, Hernández-Zavala A, Córdova EJ. Genetic alterations in the BCR-ABL1 fusion gene related to imatinib resistance in chronic myeloid leukemia. Leuk Res 2023; 131:107325. [PMID: 37302352 DOI: 10.1016/j.leukres.2023.107325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023]
Abstract
Use of the potent tyrosine kinase inhibitor imatinib as the first-line treatment in chronic myeloid leukemia (CML) has decreased mortality from 20% to 2%. Approximately 30% of CML patients experience imatinib resistance, however, largely because of point mutations in the kinase domain of the BCR-ABL1 fusion gene. The aim of this study was to use next-generation sequencing (NGS) to identify mutations related to imatinib resistance. The study included 22 patients diagnosed with CML and experiencing no clinical response to imatinib. Total RNA was used for cDNA synthesis, with amplification of a fragment encompassing the BCR-ABL1 kinase domain using a nested-PCR approach. Sanger and NGS were applied to detect genetic alterations. HaplotypeCaller was used for variant calling, and STAR-Fusion software was applied for fusion breakpoint identification. After sequencing analysis, F311I, F317L, and E450K mutations were detected respectively in three different participants, and in another two patients, single nucleotide variants in BCR (rs9608100, rs140506, rs16802) and ABL1 (rs35011138) were detected. Eleven patients carried e14a2 transcripts, nine had e13a2 transcripts, and both transcripts were identified in one patient. One patient had co-expression of e14a2 and e14a8 transcripts. The results identify candidate single nucleotide variants and co-expressed BCR-ABL1 transcripts in cellular resistance to imatinib.
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Affiliation(s)
- Macario Martínez-Castillo
- Section of Research and Postgraduate Studies, Superior School of Medicine, National Institute Polytechnique, Casco de Santo Tomás, 11350 Mexico City, Mexico
| | - Laura Gómez-Romero
- Bioinformatics Department, National Institute of Genomic Medicine, Arenal Tepepan, 14610 Mexico City, Mexico
| | - Hugo Tovar
- Computational Genomics Division, National Institute of Genomic Medicine, Arenal Tepepan, 14610 Mexico City, Mexico
| | - Irma Olarte-Carrillo
- Molecular Biology Laboratory, Service of Hematology, Hospital General de Mexico "Dr. Eduardo Licega" Dr Balmis, 06720 Mexico City, Mexico
| | - Anel García-Laguna
- Molecular Biology Laboratory, Service of Hematology, Hospital General de Mexico "Dr. Eduardo Licega" Dr Balmis, 06720 Mexico City, Mexico
| | - Gilberto Barranco-Lampón
- Molecular Biology Laboratory, Service of Hematology, Hospital General de Mexico "Dr. Eduardo Licega" Dr Balmis, 06720 Mexico City, Mexico
| | - Adrián De la Cruz-Rosas
- Molecular Biology Laboratory, Service of Hematology, Hospital General de Mexico "Dr. Eduardo Licega" Dr Balmis, 06720 Mexico City, Mexico
| | - Adolfo Martínez-Tovar
- Molecular Biology Laboratory, Service of Hematology, Hospital General de Mexico "Dr. Eduardo Licega" Dr Balmis, 06720 Mexico City, Mexico
| | - Araceli Hernández-Zavala
- Section of Research and Postgraduate Studies, Superior School of Medicine, National Institute Polytechnique, Casco de Santo Tomás, 11350 Mexico City, Mexico
| | - Emilio J Córdova
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Clinic Research, Arenal Tepepan, 14610 Mexico City, Mexico.
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Dalle Fratte C, Guardascione M, De Mattia E, Borsatti E, Boschetto R, Farruggio A, Canzonieri V, Romanato L, Borsatti R, Gagno S, Marangon E, Polano M, Buonadonna A, Toffoli G, Cecchin E. Clonal Selection of a Novel Deleterious TP53 Somatic Mutation Discovered in ctDNA of a KIT/PDGFRA Wild-Type Gastrointestinal Stromal Tumor Resistant to Imatinib. Front Pharmacol 2020; 11:36. [PMID: 32116712 PMCID: PMC7019050 DOI: 10.3389/fphar.2020.00036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/14/2020] [Indexed: 12/20/2022] Open
Abstract
The standard of care for the first-line treatment of advanced gastrointestinal stromal tumor (GIST) is represented by imatinib, which is given daily at a standard dosage until tumor progression. Resistance to imatinib commonly occurs through the clonal selection of genetic mutations in the tumor DNA, and an increase in imatinib dosage was demonstrated to be efficacious to overcome imatinib resistance. Wild-type GISTs, which do not display KIT or platelet-derived growth factor receptor alpha (PDGFRA) mutations, are usually primarily insensitive to imatinib and tend to rapidly relapse in course of treatment. Here we report the case of a 53-year-old male patient with gastric GIST who primarily did not respond to imatinib and that, despite the administration of an increased imatinib dose, led to patient death. By using a deep next-generation sequencing barcode-aware approach, we analyzed a panel of actionable cancer-related genes in the patient cfDNA to investigate somatic changes responsible for imatinib resistance. We identified, in two serial circulating tumor DNA (ctDNA) samples, a sharp increase in the allele frequency of a never described TP53 mutation (c.560-7_560-2delCTCTTAinsT) located in a splice acceptor site and responsible for a protein loss of function. The same TP53 mutation was retrospectively identified in the primary tumor by digital droplet PCR at a subclonal frequency (0.1%). The mutation was detected at a very high allelic frequency (99%) in the metastatic hepatic lesion, suggesting a rapid clonal selection of the mutation during tumor progression. Imatinib plasma concentration at steady state was above the threshold of 760 ng/ml reported in the literature for the minimum efficacious concentration. The de novo TP53 (c.560-7_560-2delCTCTTAinsT) mutation was in silico predicted to be associated with an aberrant RNA splicing and with an aggressive phenotype which might have contributed to a rapid disease spread despite the administration of an increased imatinib dosage. This result underlies the need of a better investigation upon the role of TP53 in the pathogenesis of GISTs and sustains the use of next-generation sequencing (NGS) in cfDNA for the identification of novel genetic markers in wild-type GISTs.
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Affiliation(s)
- Chiara Dalle Fratte
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Michela Guardascione
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Elena De Mattia
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Eugenio Borsatti
- Nuclear Medicine Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | | | | | - Vincenzo Canzonieri
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Loredana Romanato
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Rachele Borsatti
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Sara Gagno
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Elena Marangon
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Angela Buonadonna
- Medical Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
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Cao J, Wei J, Yang P, Zhang T, Chen Z, He F, Wei F, Chen H, Hu H, Zhong J, Yang Z, Cai W, Li W, Wang Q. Genome-scale CRISPR-Cas9 knockout screening in gastrointestinal stromal tumor with Imatinib resistance. Mol Cancer 2018; 17:121. [PMID: 30103756 PMCID: PMC6090611 DOI: 10.1186/s12943-018-0865-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/25/2018] [Indexed: 11/18/2022] Open
Abstract
Genome-scale CRISPR-Cas9 Knockout Screening was applied to investigate novel targets in imatinib-resistant gastrointestinal stromal tumor (GIST). 20 genes and 2 miRNAs have been selected by total reads of sgRNA and sgRNA diversity, which has been further validated in imatinib-resistant GIST cells by CCK8 and qPCR analysis. Our study has finally revealed 9 genes (DBP, NR3C1, TCF12, TP53, ZNF12, SOCS6, ZFP36, ACYP1, and DRD1) involved in imatinib-resistant GIST-T1 cells. TP53 and SOCS6 may be the most promising candidate genes for imatinib-resistance due to the possible signaling pathway, such as apoptosis pathway and Wnt signaling pathway, JAK-STAT signaling pathway. It is necessary to perform more studies to discover novel targets in imatinib-resistant GIST, including DBP, NR3C1, TCF12, ZNF12, ZFP36, ACYP1 and DRD1.
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Affiliation(s)
- Jie Cao
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China.
| | - Jianchang Wei
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Ping Yang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Tong Zhang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Zhuanpeng Chen
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Feng He
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Fang Wei
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Huacui Chen
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - He Hu
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Junbin Zhong
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Zhi Yang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Wensong Cai
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Wanglin Li
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China.
| | - Qiang Wang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, the Second Affiliated Hospital of South China University of Technology, 1 Panfu Road, Guangzhou, 510180, Guangdong, China.
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