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Cruz-Rodriguez N, Tang H, Bateman B, Tang W, Deininger M. BCR::ABL1 Proteolysis-targeting chimeras (PROTACs): The new frontier in the treatment of Ph + leukemias? Leukemia 2024:10.1038/s41375-024-02365-w. [PMID: 39098922 DOI: 10.1038/s41375-024-02365-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/19/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
BCR::ABL1 tyrosine kinase inhibitors (TKIs) have turned chronic myeloid leukemia (CML) from a lethal condition into a chronic ailment. With optimal management, the survival of CML patients diagnosed in the chronic phase is approaching that of age-matched controls. However, only one-third of patients can discontinue TKIs and enter a state of functional cure termed treatment-free remission (TFR), while the remainder require life-long TKI therapy to avoid the recurrence of active leukemia. Approximately 10% of patients exhibit primary or acquired TKI resistance and eventually progress to the blast phase. It is thought that recurrence after attempted TFR originates from CML stem cells (LSCs) surviving despite continued suppression of BCR::ABL1 kinase. Although kinase activity is indispensable for induction of overt CML, kinase-independent scaffold functions of BCR::ABL1 are known to contribute to leukemogenesis, raising the intriguing but as yet hypothetical possibility, that degradation of BCR::ABL1 protein may accomplish what TKIs fail to achieve - eliminate residual LSCs to turn functional into real cures. The advent of BCR::ABL1 proteolysis targeting chimeras (PROTACs), heterobifunctional molecules linking a TKI-based warhead to an E3 ligase recruiter, has moved clinical protein degradation into the realm of the possible. Here we examine the molecular rationale as well as pros and cons of degrading BCR::ABL1 protein. We review reported BCR::ABL1 PROTACs, point out limitations of available data and compounds and suggest directions for future research. Ultimately, clinical testing of a potent and specific BCR::ABL1 degrader will be required to determine the efficacy and tolerability of this approach.
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Affiliation(s)
| | - Hua Tang
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Weiping Tang
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Deininger
- Versiti Blood Research Institute, Milwaukee, WI, USA.
- Medical College of Wisconsin, Milwaukee, WI, USA.
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2
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de Azevedo LD, Leite DI, de Oliveira AP, Junior FPS, Dantas RF, Bastos MM, Boechat N, Pimentel LCF. Spirooxadiazoline-oxindoles derived from imatinib show antimyeloproliferative potential in K562 cells. Arch Pharm (Weinheim) 2024; 357:e2400029. [PMID: 38627294 DOI: 10.1002/ardp.202400029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 08/06/2024]
Abstract
Imatinib mesylate was the first representative BCR-ABL1 tyrosine kinase inhibitor (TKI) class for the treatment of chronic myeloid leukemia. Despite the revolution promoted by TKIs in the treatment of this pathology, a resistance mechanism occurs against all BCR-ABL1 inhibitors, necessitating a constant search for new therapeutic options. To develop new antimyeloproliferative substances, we applied a medicinal chemistry tool known as molecular hybridization to design 25 new substances. These compounds were synthesized and biologically evaluated against K562 cells, which express BCR-ABL1, a constitutively active tyrosine kinase enzyme, as well as in WSS-1 cells (healthy cells). The new compounds are conjugated hybrids that contain phenylamino-pyrimidine-pyridine (PAPP) and an isatin backbone, which are the main pharmacophoric fragments of imatinib and sunitinib, respectively. A spiro-oxindole nucleus was used as a linker because it occurs in many compounds with antimyeloproliferative activity. Compounds 2a, 2b, 3c, 4c, and 4e showed promise, as they inhibited cell viability by between 45% and 61% at a concentration of 10 µM. The CC50 of the most active substances was determined to be within 0.8-9.8 µM.
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MESH Headings
- Humans
- K562 Cells
- Imatinib Mesylate/pharmacology
- Oxindoles/pharmacology
- Oxindoles/chemical synthesis
- Oxindoles/chemistry
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Cell Survival/drug effects
- Structure-Activity Relationship
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/chemical synthesis
- Protein Kinase Inhibitors/chemistry
- Cell Proliferation/drug effects
- Molecular Structure
- Dose-Response Relationship, Drug
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/metabolism
- Spiro Compounds/pharmacology
- Spiro Compounds/chemistry
- Spiro Compounds/chemical synthesis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Drug Screening Assays, Antitumor
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Affiliation(s)
- Liviane D de Azevedo
- Departamento de Síntese Orgânica, Fundação Oswaldo Cruz, Farmanguinhos, Rio de Janeiro, Brasil
| | - Debora I Leite
- Departamento de Síntese Orgânica, Fundação Oswaldo Cruz, Farmanguinhos, Rio de Janeiro, Brasil
| | - Andressa P de Oliveira
- Departamento de Síntese Orgânica, Fundação Oswaldo Cruz, Farmanguinhos, Rio de Janeiro, Brasil
| | - Floriano P S Junior
- Fundação Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Rio de Janeiro, Brasil
| | - Rafael F Dantas
- Fundação Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Rio de Janeiro, Brasil
| | - Monica M Bastos
- Departamento de Síntese Orgânica, Fundação Oswaldo Cruz, Farmanguinhos, Rio de Janeiro, Brasil
| | - Nubia Boechat
- Departamento de Síntese Orgânica, Fundação Oswaldo Cruz, Farmanguinhos, Rio de Janeiro, Brasil
| | - Luiz C F Pimentel
- Departamento de Síntese Orgânica, Fundação Oswaldo Cruz, Farmanguinhos, Rio de Janeiro, Brasil
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3
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Szelest M, Giannopoulos K. Biological relevance of alternative splicing in hematologic malignancies. Mol Med 2024; 30:62. [PMID: 38760666 PMCID: PMC11100220 DOI: 10.1186/s10020-024-00839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024] Open
Abstract
Alternative splicing (AS) is a strictly regulated process that generates multiple mRNA variants from a single gene, thus contributing to proteome diversity. Transcriptome-wide sequencing studies revealed networks of functionally coordinated splicing events, which produce isoforms with distinct or even opposing functions. To date, several mechanisms of AS are deregulated in leukemic cells, mainly due to mutations in splicing and/or epigenetic regulators and altered expression of splicing factors (SFs). In this review, we discuss aberrant splicing events induced by mutations affecting SFs (SF3B1, U2AF1, SRSR2, and ZRSR2), spliceosome components (PRPF8, LUC7L2, DDX41, and HNRNPH1), and epigenetic modulators (IDH1 and IDH2). Finally, we provide an extensive overview of the biological relevance of aberrant isoforms of genes involved in the regulation of apoptosis (e. g. BCL-X, MCL-1, FAS, and c-FLIP), activation of key cellular signaling pathways (CASP8, MAP3K7, and NOTCH2), and cell metabolism (PKM).
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Affiliation(s)
- Monika Szelest
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland.
| | - Krzysztof Giannopoulos
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland
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4
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Shi H, Gao L, Zhang W, Jiang M. Long non-coding RNAs regulate treatment outcome in leukemia: What have we learnt recently? Cancer Med 2023. [PMID: 37148556 DOI: 10.1002/cam4.6027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/08/2023] Open
Abstract
Leukemia is a group of highly heterogeneous and life-threatening blood cancers that originate from abnormal hematopoietic stem cells. Multiple treatments are approved for leukemia, including chemotherapy, targeted therapy, hematopoietic stem cell transplantation, radiation therapy, and immunotherapy. Unfortunately, therapeutic resistance occurs in a substantial proportion of patients and greatly compromises the treatment efficacy of leukemia, resulting in relapse and mortality. The abnormal activity of receptor tyrosine kinases, cell membrane transporters, intracellular signal transducers, transcription factors, and anti-apoptotic proteins have been shown to contribute to the emergence of therapeutic resistance. Despite these findings, the exact mechanisms of treatment resistance are still not fully understood, which limits the development of effective measures to overcome it. Long non-coding RNAs (lncRNA) are a class of regulatory molecules that are gaining increasing attention, and lncRNA-mediated regulation of therapeutic resistance against multiple drugs for leukemia is being revealed. These dysregulated lncRNAs not only serve as potential targets to reduce resistance but also might improve treatment response prediction and individualized treatment decision. Here, we summarize the recent findings on lncRNA-mediated regulation of therapeutic resistance in leukemia and discuss future perspectives on how to make use of the dysregulated lncRNAs in leukemia to improve treatment outcome.
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Affiliation(s)
- Huiping Shi
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Liang Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Weili Zhang
- Department of Gastroenterology, Xiangcheng People's Hospital, Suzhou, Jiangsu, People's Republic of China
| | - Min Jiang
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
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Feng L, Ding R, Qu X, Li Y, Shen T, Wang L, Li R, Zhang J, Ru Y, Bu X, Wang Y, Li M, Song W, Shen L, Zhang P. BCR-ABL triggers a glucose-dependent survival program during leukemogenesis through the suppression of TXNIP. Cell Death Dis 2023; 14:287. [PMID: 37095099 PMCID: PMC10125982 DOI: 10.1038/s41419-023-05811-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/04/2023] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
Imatinib is highly effective in the treatment of chronic myelogenous leukemia (CML), but the primary and acquired imatinib resistance remains the big hurdle. Molecular mechanisms for CML resistance to tyrosine kinase inhibitors, beyond point mutations in BCR-ABL kinase domain, still need to be addressed. Here, we demonstrated that thioredoxin-interacting protein (TXNIP) is a novel BCR-ABL target gene. Suppression of TXNIP was responsible for BCR-ABL triggered glucose metabolic reprogramming and mitochondrial homeostasis. Mechanistically, Miz-1/P300 complex transactivates TXNIP through the recognition of TXNIP core promoter region, responding to the c-Myc suppression by either imatinib or BCR-ABL knockdown. TXNIP restoration sensitizes CML cells to imatinib treatment and compromises imatinib resistant CML cell survival, predominantly through the blockage of both glycolysis and glucose oxidation which results in the mitochondrial dysfunction and ATP production. In particular, TXNIP suppresses expressions of the key glycolytic enzyme, hexokinase 2 (HK2), and lactate dehydrogenase A (LDHA), potentially through Fbw7-dependent c-Myc degradation. In accordance, BCR-ABL suppression of TXNIP provided a novel survival pathway for the transformation of mouse bone marrow cells. Knockout of TXNIP accelerated BCR-ABL transformation, whereas TXNIP overexpression suppressed this transformation. Combination of drug inducing TXNIP expression with imatinib synergistically kills CML cells from patients and further extends the survival of CML mice. Thus, the activation of TXNIP represents an effective strategy for CML treatment to overcome resistance.
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Affiliation(s)
- Lin Feng
- Key Laboratory of Microecology-immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang, China
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Ruxin Ding
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Xuan Qu
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yuanchun Li
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Tong Shen
- Department of Digestive Surgery, Xi'an International Medical Center, Xi'an, China
| | - Lei Wang
- Xi'an Beihuan Hospital, Xi'an, China
| | - Ruikai Li
- Department of Gastrointestinal Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Juan Zhang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Northwest University, Xi'an, China
| | - Yi Ru
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Xin Bu
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Yang Wang
- Tongchuan People's Hospital, Tongchuan, China
| | - Min Li
- Xi'an Eastern Hospital, Xi'an, China
| | - Wenqi Song
- Jiamusi Maternal and Child Health Care Hospital, Jiamusi, Heilongjiang, China
| | - Liangliang Shen
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China.
| | - Pengxia Zhang
- Key Laboratory of Microecology-immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang, China.
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6
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Liu ZC, Li LH, Li DY, Gao ZQ, Chen D, Song B, Jiang BH, Dang XW. KIAA1429 regulates alternative splicing events of cancer-related genes in hepatocellular carcinoma. Front Oncol 2022; 12:1060574. [PMID: 36505780 PMCID: PMC9732450 DOI: 10.3389/fonc.2022.1060574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains one of the most fatal malignancies with high morbidity and mortality rates in the world, whose molecular pathogenesis is incompletely understood. As an RNA-binding protein participating in the processing and modification of RNA, KIAA1429 has been proved to be implicated in the pathogenesis of multiple cancers. However, how KIAA1429 functions in alternative splicing is not fully reported. In the current study, multi-omics sequencing data were used to analyze and decipher the molecular functions and the underlying mechanisms of KIAA1429 in HCC samples. RNA sequencing data (RNA-seq) analysis demonstrated that in HCCLM3 cells, alternative splicing (AS) profiles were mediated by KIAA1429. Regulated AS genes (RASGs) by KIAA1429 were enriched in cell cycle and apoptosis-associated pathways. Furthermore, by integrating the RNA immunoprecipitation and sequencing data (RIP-seq) of KIAA1429, we found that KIAA1429-bound transcripts were highly overlapping with RASGs, indicating that KIAA1429 could globally regulate the alternative splicing perhaps by binding to their transcripts in HCCLM3 cells. The overlapping RASGs were also clustered in cell cycle and apoptosis-associated pathways. In particular, we validated the regulated AS events of three genes using clinical specimens from HCC patients, including the exon 6 of BPTF gene and a marker gene of HCC. In summary, our results shed light on the regulatory functions of KIAA1429 in the splicing process of pre-mRNA and provide theoretical basis for the targeted therapy of HCC.
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Affiliation(s)
- Zhao-chen Liu
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lu-Hao Li
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ding-Yang Li
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhi-Qiang Gao
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co. Ltd, Zhengzhou, China
| | - Bin Song
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co. Ltd, Zhengzhou, China
| | - Bing-Hua Jiang
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiao-wei Dang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Xiao-wei Dang,
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7
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Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol 2022; 12:1051487. [PMID: 36505834 PMCID: PMC9730332 DOI: 10.3389/fonc.2022.1051487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer-specific alternatively spliced events (ASE) play a role in cancer pathogenesis and can be targeted by immunotherapy, oligonucleotide therapy, and small molecule inhibition. However, identifying actionable ASE targets remains challenging due to the uncertainty of its protein product, structure impact, and proteoform (protein isoform) function. Here we argue that an integrated multi-omics profiling strategy can overcome these challenges, allowing us to mine this untapped source of targets for therapeutic development. In this review, we will provide an overview of current multi-omics strategies in characterizing ASEs by utilizing the transcriptome, proteome, and state-of-art algorithms for protein structure prediction. We will discuss limitations and knowledge gaps associated with each technology and informatics analytics. Finally, we will discuss future directions that will enable the full integration of multi-omics data for ASE target discovery.
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Affiliation(s)
- Timothy I. Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States,*Correspondence: Timothy I. Shaw,
| | - Bi Zhao
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Brandon Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Aleksandra Karolak
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
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8
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Venkataramany AS, Schieffer KM, Lee K, Cottrell CE, Wang PY, Mardis ER, Cripe TP, Chandler DS. Alternative RNA Splicing Defects in Pediatric Cancers: New Insights in Tumorigenesis and Potential Therapeutic Vulnerabilities. Ann Oncol 2022; 33:578-592. [PMID: 35339647 DOI: 10.1016/j.annonc.2022.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Compared to adult cancers, pediatric cancers are uniquely characterized by a genomically stable landscape and lower tumor mutational burden. However, alternative splicing, a global cellular process that produces different mRNA/protein isoforms from a single mRNA transcript, has been increasingly implicated in the development of pediatric cancers. DESIGN We review the current literature on the role of alternative splicing in adult cancer, cancer predisposition syndromes, and pediatric cancers. We also describe multiple splice variants identified in adult cancers and confirmed through comprehensive genomic profiling in our institutional cohort of rare, refractory and relapsed pediatric and adolescent young adult cancer patients. Finally, we summarize the contributions of alternative splicing events to neoantigens and chemoresistance and prospects for splicing-based therapies. RESULTS Published dysregulated splicing events can be categorized as exon inclusion, exon exclusion, splicing factor upregulation, or splice site alterations. We observe these phenomena in cancer predisposition syndromes (Lynch syndrome, Li-Fraumeni syndrome, CHEK2) and pediatric leukemia (B-ALL), sarcomas (Ewing sarcoma, rhabdomyosarcoma, osteosarcoma), retinoblastoma, Wilms tumor, and neuroblastoma. Within our institutional cohort, we demonstrate splice variants in key regulatory genes (CHEK2, TP53, PIK3R1, MDM2, KDM6A, NF1) that resulted in exon exclusion or splice site alterations, which were predicted to impact functional protein expression and promote tumorigenesis. Differentially spliced isoforms and splicing proteins also impact neoantigen creation and treatment resistance, such as imatinib or glucocorticoid regimens. Additionally, splice-altering strategies with the potential to change the therapeutic landscape of pediatric cancers include antisense oligonucleotides, adeno-associated virus gene transfers, and small molecule inhibitors. CONCLUSIONS Alternative splicing plays a critical role in the formation and growth of pediatric cancers, and our institutional cohort confirms and highlights the broad spectrum of affected genes in a variety of cancers. Further studies that elucidate the mechanisms of disease-inducing splicing events will contribute toward the development of novel therapeutics.
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Affiliation(s)
- A S Venkataramany
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States; Medical Scientist Training Program, The Ohio State University, Columbus, Ohio, United States
| | - K M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States
| | - K Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - C E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - P Y Wang
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States
| | - E R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - T P Cripe
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States; Division of Hematology, Oncology and Blood and Marrow Transplant, Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States
| | - D S Chandler
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States; Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States.
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9
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Impact of alternative splicing on mechanisms of resistance to anticancer drugs. Biochem Pharmacol 2021; 193:114810. [PMID: 34673012 DOI: 10.1016/j.bcp.2021.114810] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
A shared characteristic of many tumors is the lack of response to anticancer drugs. Multiple mechanisms of pharmacoresistance (MPRs) are involved in permitting cancer cells to overcome the effect of these agents. Pharmacoresistance can be primary (intrinsic) or secondary (acquired), i.e., triggered or enhanced in response to the treatment. Moreover, MPRs usually result in the lack of sensitivity to several agents, which accounts for diverse multidrug-resistant (MDR) phenotypes. MPRs are based on the dynamic expression of more than one hundred genes, constituting the so-called resistome. Alternative splicing (AS) during pre-mRNA maturation results in changes affecting proteins involved in the resistome. The resulting splicing variants (SVs) reduce the efficacy of anticancer drugs by lowering the intracellular levels of active agents, altering molecular targets, enhancing both DNA repair ability and defensive mechanism of tumors, inducing changes in the balance between pro-survival and pro-apoptosis signals, modifying interactions with the tumor microenvironment, and favoring malignant phenotypic transitions. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the impact of AS on MPR in cancer cells.
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10
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Resistance to Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia-From Molecular Mechanisms to Clinical Relevance. Cancers (Basel) 2021; 13:cancers13194820. [PMID: 34638304 PMCID: PMC8508378 DOI: 10.3390/cancers13194820] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Chronic myeloid leukemia (CML) is a myeloproliferative neoplasia associated with a molecular alteration, the fusion gene BCR-ABL1, that encodes the tyrosine kinase oncoprotein BCR-ABL1. This led to the development of tyrosine kinase inhibitors (TKI), with Imatinib being the first TKI approved. Although the vast majority of CML patients respond to Imatinib, resistance to this targeted therapy contributes to therapeutic failure and relapse. Here we review the molecular mechanisms and other factors (e.g., patient adherence) involved in TKI resistance, the methodologies to access these mechanisms, and the possible therapeutic approaches to circumvent TKI resistance in CML. Abstract Resistance to targeted therapies is a complex and multifactorial process that culminates in the selection of a cancer clone with the ability to evade treatment. Chronic myeloid leukemia (CML) was the first malignancy recognized to be associated with a genetic alteration, the t(9;22)(q34;q11). This translocation originates the BCR-ABL1 fusion gene, encoding the cytoplasmic chimeric BCR-ABL1 protein that displays an abnormally high tyrosine kinase activity. Although the vast majority of patients with CML respond to Imatinib, a tyrosine kinase inhibitor (TKI), resistance might occur either de novo or during treatment. In CML, the TKI resistance mechanisms are usually subdivided into BCR-ABL1-dependent and independent mechanisms. Furthermore, patients’ compliance/adherence to therapy is critical to CML management. Techniques with enhanced sensitivity like NGS and dPCR, the use of artificial intelligence (AI) techniques, and the development of mathematical modeling and computational prediction methods could reveal the underlying mechanisms of drug resistance and facilitate the design of more effective treatment strategies for improving drug efficacy in CML patients. Here we review the molecular mechanisms and other factors involved in resistance to TKIs in CML and the new methodologies to access these mechanisms, and the therapeutic approaches to circumvent TKI resistance.
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11
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Tadesse F, Asres G, Abubeker A, Gebremedhin A, Radich J. Spectrum of BCR-ABL Mutations and Treatment Outcomes in Ethiopian Imatinib-Resistant Patients With Chronic Myeloid Leukemia. JCO Glob Oncol 2021; 7:1187-1193. [PMID: 34292760 PMCID: PMC8457809 DOI: 10.1200/go.21.00058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the successes achieved in chronic myeloid leukemia (CML) with tyrosine kinase inhibitor (TKI) therapy, resistance remains an obstacle. The most common mechanism of resistance is the acquisition of a point mutation in the BCR-ABL kinase domain. Few studies have reported African patients with CML in regard to such mutations. We here report the types of BCR-ABL mutations in Ethiopian imatinib-resistant patients with CML and their outcome.
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Affiliation(s)
| | - Getahun Asres
- University of Gondar, College of Medicine and Health Sciences, Gondar, Ethiopia
| | - Abdulaziz Abubeker
- Addis Ababa University College of Health Sciences, Addis Ababa, Ethiopia
| | - Amha Gebremedhin
- Addis Ababa University College of Health Sciences, Addis Ababa, Ethiopia
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12
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Minati R, Perreault C, Thibault P. A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens. Front Immunol 2020; 11:583287. [PMID: 33424836 PMCID: PMC7793940 DOI: 10.3389/fimmu.2020.583287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
The search for tumor-specific antigens (TSAs) has considerably accelerated during the past decade due to the improvement of proteogenomic detection methods. This provides new opportunities for the development of novel antitumoral immunotherapies to mount an efficient T cell response against one or multiple types of tumors. While the identification of mutated antigens originating from coding exons has provided relatively few TSA candidates, the possibility of enlarging the repertoire of targetable TSAs by looking at antigens arising from non-canonical open reading frames opens up interesting avenues for cancer immunotherapy. In this review, we outline the potential sources of TSAs and the mechanisms responsible for their expression strictly in cancer cells. In line with the heterogeneity of cancer, we propose that discrete families of TSAs may be enriched in specific cancer types.
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Affiliation(s)
- Robin Minati
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
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13
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Liu J, Zhang Y, Huang H, Lei X, Tang G, Cao X, Peng J. Recent advances in Bcr-Abl tyrosine kinase inhibitors for overriding T315I mutation. Chem Biol Drug Des 2020; 97:649-664. [PMID: 33034143 DOI: 10.1111/cbdd.13801] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 09/13/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
BCR-ABL is a gene produced by the fusion of the bcr gene and the c-abl proto-oncogene and is considered to be the main cause of chronic myelogenous leukemia (CML) production. Therefore, the development of selective Bcr-Abl kinase inhibitors is an attractive strategy for the treatment of CML. However, in the treatment of CML with a Bcr-Abl kinase inhibitor, the T315I gatekeeper mutant disrupts the important contact interaction between the inhibitor and the enzyme, resistant to the first- and second-generation drugs currently approved, such as imatinib, bosutinib, nilotinib, and dasatinib. In order to overcome this special resistance, several different strategies have been explored, and many molecules have been studied to effectively inhibit Bcr-Abl T315I. Some of these molecules are still under development, and some are being studied preclinically, and still others are in clinical research. Herein, this review reports some of the major examples of third-generation Bcr-Abl inhibitors against the T315I mutation.
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Affiliation(s)
- Juan Liu
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China.,Pharmacy Department of Yiyang Central Hospital, Yiyang, China
| | - Yuan Zhang
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Honglin Huang
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Xiaoyong Lei
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Guotao Tang
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
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14
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Wang E, Aifantis I. RNA Splicing and Cancer. Trends Cancer 2020; 6:631-644. [PMID: 32434734 DOI: 10.1016/j.trecan.2020.04.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/01/2023]
Abstract
RNA splicing is an essential process that governs many aspects of cellular proliferation, survival, and differentiation. Considering the importance of RNA splicing in gene regulation, alterations in this pathway have been implicated in many human cancers. Large-scale genomic studies have uncovered a spectrum of splicing machinery mutations that contribute to tumorigenesis. Moreover, cancer cells are capable of hijacking the expression of RNA-binding proteins (RBPs), leading to dysfunctional gene splicing and tumor-specific dependencies. Advances in next-generation RNA sequencing have revealed tumor-specific isoforms associated with these alterations, including the presence of neoantigens, which serve as potential immunotherapeutic targets. In this review, we discuss the various mechanisms by which cancer cells exploit RNA splicing to promote tumor growth and the current therapeutic landscape for splicing-based therapies.
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Affiliation(s)
- Eric Wang
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
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15
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Yuda J, Odawara J, Minami M, Muta T, Kohno K, Tanimoto K, Eto T, Shima T, Kikushige Y, Kato K, Takenaka K, Iwasaki H, Minami Y, Ohkawa Y, Akashi K, Miyamoto T. Tyrosine kinase inhibitors induce alternative spliced BCR-ABL Ins35bp variant via inhibition of RNA polymerase II on genomic BCR-ABL. Cancer Sci 2020; 111:2361-2373. [PMID: 32314454 PMCID: PMC7385367 DOI: 10.1111/cas.14424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/16/2020] [Accepted: 03/22/2020] [Indexed: 11/28/2022] Open
Abstract
To elucidate dynamic changes in native BCR-ABL and alternatively spliced tyrosine kinase inhibitor (TKI)-resistant but function-dead BCR-ABLIns35bp variant, following commencement or discontinuation of TKI therapy, each transcript was serially quantified in patients with chronic myeloid leukemia (CML) by deep sequencing. Because both transcripts were amplified together using conventional PCR system for measuring International Scale (IS), deep sequencing method was used for quantifying such BCR-ABL variants. At the initial diagnosis, 7 of 9 patients presented a small fraction of cells possessing BCR-ABLIns35bp , accounting for 0.8% of the total IS BCR-ABL, corresponding to actual BCR-ABLIns35bp value of 1.1539% IS. TKI rapidly decreased native BCR-ABL but not BCR-ABLIns35bp , leading to the initial increase in the proportion of BCR-ABLIns35bp . Thereafter, both native BCR-ABL and BCR-ABLIns35bp gradually decreased in the course of TKI treatment, whereas small populations positive for TKI-resistant BCR-ABLIns35bp continued fluctuating at low levels, possibly underestimating the molecular response (MR). Following TKI discontinuation, sequencing analysis of 54 patients revealed a rapid relapse, apparently derived from native BCR-ABL+ clones. However, IS fluctuating at low levels around MR4.0 marked a predominant persistence of cells expressing function-dead BCR-ABLIns35bp , suggesting that TKI resumption was unnecessary. We clarified the possible mechanism underlying mis-splicing BCR-ABLIns35bp , occurring at the particular pseudo-splice site within intron8, which can be augmented by TKI treatment through inhibition of RNA polymerase II phosphorylation. No mutations were found in spliceosomal genes. Therefore, monitoring IS functional BCR-ABL extracting BCR-ABLIns35bp would lead us to a correct evaluation of MR status, thus determining the adequate therapeutic intervention.
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Affiliation(s)
- Junichiro Yuda
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Jun Odawara
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Mariko Minami
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Tsuyoshi Muta
- Department of Hematology and Oncology, Japan Community Health Care Organization Kyushu Hospital, Fukuoka, Japan
| | - Kentaro Kohno
- Department of Hematology and Clinical Research Institute, National Hospital Organization Kyushu Medical Center, Fukuoka, Japan
| | - Kazuki Tanimoto
- Department of Haematology and Oncology, Japanese Red Cross Society Fukuoka Red Cross Hospital, Fukuoka, Japan
| | - Tetsuya Eto
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Takahiro Shima
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Yoshikane Kikushige
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Katsuto Takenaka
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Hiromi Iwasaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Kyushu University, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Toshihiro Miyamoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
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16
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Roles and mechanisms of alternative splicing in cancer - implications for care. Nat Rev Clin Oncol 2020; 17:457-474. [PMID: 32303702 DOI: 10.1038/s41571-020-0350-x] [Citation(s) in RCA: 367] [Impact Index Per Article: 91.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
Removal of introns from messenger RNA precursors (pre-mRNA splicing) is an essential step for the expression of most eukaryotic genes. Alternative splicing enables the regulated generation of multiple mRNA and protein products from a single gene. Cancer cells have general as well as cancer type-specific and subtype-specific alterations in the splicing process that can have prognostic value and contribute to every hallmark of cancer progression, including cancer immune responses. These splicing alterations are often linked to the occurrence of cancer driver mutations in genes encoding either core components or regulators of the splicing machinery. Of therapeutic relevance, the transcriptomic landscape of cancer cells makes them particularly vulnerable to pharmacological inhibition of splicing. Small-molecule splicing modulators are currently in clinical trials and, in addition to splice site-switching antisense oligonucleotides, offer the promise of novel and personalized approaches to cancer treatment.
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17
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Wei X, He L, Wang X, Lin M, Dai J. Effects of dasatinib on CD8 +T, Th1, and Treg cells in patients with chronic myeloid leukemia. J Int Med Res 2020; 48:300060519877321. [PMID: 31578901 PMCID: PMC7607186 DOI: 10.1177/0300060519877321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/29/2019] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To investigate the immunomodulatory effects of the tyrosine kinase inhibitor (TKI) dasatinib on T-cell subtypes in patients with chronic myeloid leukemia (CML). METHODS T helper (Th) 1, Th2, regulatory T (Treg), and CD8+T cell levels were detected in patients with CML (n = 9) before and after dasatinib treatment. The corresponding response level at the time of a blood test was evaluated. RESULTS After dasatinib treatment, six patients achieved a better response level, while three did not show improved response levels. Among the total nine patients, there were no significant differences in Th1, Th2, and Treg cell levels, whereas CD8+T cell levels were significantly increased after dasatinib treatment compared with before treatment. When we analyzed the six patients who obtained a better response level, Th1 and CD8+T cell levels were significantly increased after dasatinib treatment, but Th2 and Treg cell levels did not change. The other three patients who did not have improved response levels showed decreased Th1 cell levels and increased Treg cell levels after treatment. CONCLUSIONS Dasatinib may increase Th1 and CD8+T cell levels, and decrease Treg cell levels in patients with CML. This finding might be associated with a good therapeutic response to this drug.
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Affiliation(s)
- Xiaoqing Wei
- Sichuan Academy of Medical Science & Sichuan
Provincial People’s Hospital, School of Medicine of University of Electronic
Science and Technology of China, Chengdu, 610072, China
| | - Lin He
- Sichuan Academy of Medical Science & Sichuan
Provincial People’s Hospital, School of Medicine of University of Electronic
Science and Technology of China, Chengdu, 610072, China
| | - Xiaodong Wang
- Sichuan Academy of Medical Science & Sichuan
Provincial People’s Hospital, School of Medicine of University of Electronic
Science and Technology of China, Chengdu, 610072, China
| | | | - Jingying Dai
- Jingying Dai, Sichuan Academy of Medical
Science & Sichuan Provincial People’s Hospital, School of Medicine of
University of Electronic Science and Technology of China, Chengdu, Sichuan
Province 610072, China.
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18
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Dong Y, Lin Y, Gao X, Zhao Y, Wan Z, Wang H, Wei M, Chen X, Qin W, Yang G, Liu L. Targeted blocking of miR328 lysosomal degradation with alkalized exosomes sensitizes the chronic leukemia cells to imatinib. Appl Microbiol Biotechnol 2019; 103:9569-9582. [PMID: 31701195 DOI: 10.1007/s00253-019-10127-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 02/05/2023]
Abstract
Imatinib resistance remains the biggest hurdle for the treatment of chronic myeloid leukemia (CML), with the underlying mechanisms not fully understood. In this study, we found that miR328 significantly and strikingly decreased among other miRNA candidates during the induction of imatinib resistance. Overexpression of miR328 sensitized resistant cells to imatinib via post-transcriptionally decreasing ABCG2 expression, while miR328 knockdown conferred imatinib resistance in parental K562 cells. Moreover, miR328 was found selectively degraded in the lysosomes of K562R cells, as inhibition of lysosome with chloroquine restored miR328 expression and increased sensitivity to imatinib. Moreover, delivery of alkalized exosomes increased endogenous miR328 expression. Compared with the corresponding controls, the alkalized exosomes with or without miR328 sensitized the chronic leukemia cells to imatinib. Taken together, our study has revealed that lysosomal clearance of miR328 in imatinib-resistant cells at least partially contributes to the drug resistance, while delivery of alkalized exosomes would sensitize the chromic leukemia cells to imatinib.
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Affiliation(s)
- Yan Dong
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Yao Lin
- Department of Stomatology, the Second Affiliated hospital, Shantou University Medical College, Shantou, China
| | - Xiaotong Gao
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Yingxin Zhao
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Zhuo Wan
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Haotian Wang
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Mengying Wei
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Changlexi Road NO.169th, Xi'an, 710032, China
| | - Xutao Chen
- Department of Implantation, School of Stomatology, Fourth Military Medical University, Xi'an, China
| | - Weiwei Qin
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Guodong Yang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Changlexi Road NO.169th, Xi'an, 710032, China.
| | - Li Liu
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China.
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19
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Neckles C, Sundara Rajan S, Caplen NJ. Fusion transcripts: Unexploited vulnerabilities in cancer? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1562. [PMID: 31407506 PMCID: PMC6916338 DOI: 10.1002/wrna.1562] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Gene fusions are an important class of mutations in several cancer types and include genomic rearrangements that fuse regulatory or coding elements from two different genes. Analysis of the genetics of cancers harboring fusion oncogenes and the proteins they encode have enhanced cancer diagnosis and in some cases patient treatment. However, the effect of the complex structure of fusion genes on the biogenesis of the resulting chimeric transcripts they express is not well studied. There are two potential RNA‐related vulnerabilities inherent to fusion‐driven cancers: (a) the processing of the fusion precursor messenger RNA (pre‐mRNA) to the mature mRNA and (b) the mature mRNA. In this study, we discuss the effects that the genetic organization of fusion oncogenes has on the generation of translatable mature RNAs and the diversity of fusion transcripts expressed in different cancer subtypes, which can fundamentally influence both tumorigenesis and treatment. We also discuss functional genomic approaches that can be utilized to identify proteins that mediate the processing of fusion pre‐mRNAs. Furthermore, we assert that an enhanced understanding of fusion transcript biogenesis and the diversity of the chimeric RNAs present in fusion‐driven cancers will increase the likelihood of successful application of RNA‐based therapies in this class of tumors. This article is categorized under:RNA Processing > RNA Editing and Modification RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
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20
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de Fraipont F, Gazzeri S, Cho WC, Eymin B. Circular RNAs and RNA Splice Variants as Biomarkers for Prognosis and Therapeutic Response in the Liquid Biopsies of Lung Cancer Patients. Front Genet 2019; 10:390. [PMID: 31134126 PMCID: PMC6514155 DOI: 10.3389/fgene.2019.00390] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/10/2019] [Indexed: 01/08/2023] Open
Abstract
Lung cancer, including non-small cell lung carcinoma (NSCLC), is the most frequently diagnosed cancer. It is also the leading cause of cancer-related mortality worldwide because of its late diagnosis and its resistance to therapies. Therefore, the identification of biomarkers for early diagnosis, prognosis, and monitoring of therapeutic response is urgently needed. Liquid biopsies, especially blood, are considered as promising tools to detect and quantify circulating cancer biomarkers. Cell-free circulating tumor DNA has been extensively studied. Recently, the possibility to detect and quantify RNAs in tumor biopsies, notably circulating cell-free RNAs, has gained great attention. RNA alternative splicing contributes to the proteome diversity through the biogenesis of several mRNA splice variants from the same pre-mRNA. Circular RNA (circRNA) is a new class of RNAs resulting from pre-mRNA back splicing. Owing to the development of high-throughput transcriptomic analyses, numerous RNA splice variants and, more recently, circRNAs have been identified and found to be differentially expressed in tumor patients compared to healthy controls. The contribution of some of these RNA splice variants and circRNAs to tumor progression, dissemination, or drug response has been clearly demonstrated in preclinical models. In this review, we discuss the potential of circRNAs and mRNA splice variants as candidate biomarkers for the prognosis and the therapeutic response of NSCLC in liquid biopsies.
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Affiliation(s)
- Florence de Fraipont
- INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
- Grenoble Hospital, La Tronche, France
| | - Sylvie Gazzeri
- INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Beatrice Eymin
- INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
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21
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Wang BD, Lee NH. Aberrant RNA Splicing in Cancer and Drug Resistance. Cancers (Basel) 2018; 10:E458. [PMID: 30463359 PMCID: PMC6266310 DOI: 10.3390/cancers10110458] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022] Open
Abstract
More than 95% of the 20,000 to 25,000 transcribed human genes undergo alternative RNA splicing, which increases the diversity of the proteome. Isoforms derived from the same gene can have distinct and, in some cases, opposing functions. Accumulating evidence suggests that aberrant RNA splicing is a common and driving event in cancer development and progression. Moreover, aberrant splicing events conferring drug/therapy resistance in cancer is far more common than previously envisioned. In this review, aberrant splicing events in cancer-associated genes, namely BCL2L1, FAS, HRAS, CD44, Cyclin D1, CASP2, TMPRSS2-ERG, FGFR2, VEGF, AR and KLF6, will be discussed. Also highlighted are the functional consequences of aberrant splice variants (BCR-Abl35INS, BIM-γ, IK6, p61 BRAF V600E, CD19-∆2, AR-V7 and PIK3CD-S) in promoting resistance to cancer targeted therapy or immunotherapy. To overcome drug resistance, we discuss opportunities for developing novel strategies to specifically target the aberrant splice variants or splicing machinery that generates the splice variants. Therapeutic approaches include the development of splice variant-specific siRNAs, splice switching antisense oligonucleotides, and small molecule inhibitors targeting splicing factors, splicing factor kinases or the aberrant oncogenic protein isoforms.
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Affiliation(s)
- Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.
| | - Norman H Lee
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, GW Cancer Center, Washington, DC 20037, USA.
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22
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Mikhailov I. BCR-ABL exon 7 deletion and novel point mutation in patient with chronic myelogenous leukemia and TKI resistance. Clin Case Rep 2018; 6:2057-2060. [PMID: 30455891 PMCID: PMC6230594 DOI: 10.1002/ccr3.1794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/28/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
I report a novel BCR-ABL point mutation c.844G>C p.E282Q and a case of combination of two BCR-ABL point mutations (p.E282Q and p.L298R) and exon 7 deletion (del. c.1086-1270) in TKI-resistant patient. These point mutations were present only in a truncated transcript and were absent in "wild-type" BCR-ABL transcript.
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Affiliation(s)
- Ilya Mikhailov
- Faculty of Fundamental MedicineLomonosov Moscow State UniversityMoscowRussian Federation
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23
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Rajabnia T, Meshkini A. Fabrication of adenosine 5′-triphosphate-capped silver nanoparticles: Enhanced cytotoxicity efficacy and targeting effect against tumor cells. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Dong Y, Gao X, Zhao Y, Wei M, Xu L, Yang G, Liu L. Semi‑random mutagenesis profile of BCR‑ABL during imatinib resistance acquirement in K562 cells. Mol Med Rep 2017; 16:9409-9414. [PMID: 29152650 PMCID: PMC5779997 DOI: 10.3892/mmr.2017.7835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/01/2017] [Indexed: 01/14/2023] Open
Abstract
Although imatinib is effective in chronic myeloid leukemia treatment, imatinib resistance due to the T315I mutation and/or other mutations is a challenge to be overcome. However, how DNA mutation occurs, particularly the T315I mutation, remains unclear. In the current study, the mutagenesis of BCR-ABL was analyzed via focusing on the process of drug resistance, rather than the final results. Clone sequencing of the BCR-ABL gene and other control genes was applied in two imatinib-resistant cell models. The results have indicated that imatinib actively and selectively causes sporadic mutations in the BCR-ABL gene, however not in the control genes. The majority of the mutations of BCR-ABL were not the clinically observed T315I mutation, suggesting that the T315I mutation may be due to clonal expansion of cells with survival advantages. Taken together, the results of the current study elucidated the mutagenesis process during drug resistance and thus aids in the management of chemotherapy.
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Affiliation(s)
- Yan Dong
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Xiaotong Gao
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Yingxin Zhao
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Mengying Wei
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Lingmin Xu
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Guodong Yang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Li Liu
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
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Yuda J, Miyamoto T, Odawara J, Ohkawa Y, Semba Y, Hayashi M, Miyamura K, Tanimoto M, Yamamoto K, Taniwaki M, Akashi K. Persistent detection of alternatively spliced BCR-ABL variant results in a failure to achieve deep molecular response. Cancer Sci 2017; 108:2204-2212. [PMID: 28801986 PMCID: PMC5666036 DOI: 10.1111/cas.13353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 01/04/2023] Open
Abstract
Treatment with tyrosine kinase inhibitors (TKI) may sequentially induce TKI‐resistant BCR‐ABL mutants in chronic myeloid leukemia (CML). Conventional PCR monitoring of BCR‐ABL is an important indicator to determine therapeutic intervention for preventing disease progression. However, PCR cannot separately quantify amounts of BCR‐ABL and its mutants, including alternatively spliced BCR‐ABL with an insertion of 35 intronic nucleotides (BCR‐ABLIns35bp) between ABL exons 8 and 9, which introduces the premature termination and loss of kinase activity. To assess the clinical impact of BCR‐ABL mutants, we performed deep sequencing analysis of BCR‐ABL transcripts of 409 samples from 37 patients with suboptimal response to frontline imatinib who were switched to nilotinib. At baseline, TKI‐resistant mutations were documented in 3 patients, whereas BCR‐ABLIns35bp was detected in all patients. After switching to nilotinib, both BCR‐ABL and BCR‐ABLIns35bp became undetectable in 3 patients who attained complete molecular response (CMR), whereas in the remaining all 34 patients, BCR‐ABLIns35bp was persistently detected, and minimal residual disease (MRD) fluctuated at low but detectable levels. PCR monitoring underestimated molecular response in 5 patients whose BCR‐ABLIns35bp was persisted, although BCR‐ABLIns35bp does not definitively mark TKI resistance. Therefore, quantification of BCR‐ABLIns35bp is useful for evaluating “functional” MRD and determining the effectiveness of TKI with accuracy.
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Affiliation(s)
- Junichiro Yuda
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Toshihiro Miyamoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Jun Odawara
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan.,Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuichiro Semba
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan.,Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masayasu Hayashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan.,Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koichi Miyamura
- Department of Hematology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Japan
| | - Mitsune Tanimoto
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama, Japan
| | - Kazuhito Yamamoto
- Department of Clinical Research and Department of Hematology and Cell Therapy, Aichi Cancer Center, Nagoya, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
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Wang H, Li Q, Tang S, Li M, Feng A, Qin L, Liu Z, Wang X. The role of long noncoding RNA HOTAIR in the acquired multidrug resistance to imatinib in chronic myeloid leukemia cells. Hematology 2016; 22:208-216. [DOI: 10.1080/10245332.2016.1258152] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
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