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Han B, Yang M, Yang X, Liu M, Xie Q, Fan G, Hosseini DK, Yu J, Song P, Chen X, Sun H. Systematic Analysis of Survival-Associated Alternative Splicing Signatures in Thyroid Carcinoma. Front Oncol 2021; 11:561457. [PMID: 34249669 PMCID: PMC8261059 DOI: 10.3389/fonc.2021.561457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is a key mechanism involved in regulating gene expression and is closely related to tumorigenesis. The incidence of thyroid cancer (THCA) has increased during the past decade, and the role of AS in THCA is still unclear. Here, we used TCGA and to generate AS maps in patients with THCA. Univariate analysis revealed 825 AS events related to the survival of THCA. Five prognostic models of AA, AD, AT, ES, and ME events were obtained through lasso and multivariate analyses, and the final prediction model was established by integrating all the AS events in the five prediction models. Kaplan–Meier survival analysis revealed that the overall survival rate of patients in the high-risk group was significantly shorter than that of patients in the low-risk group. The ROC results revealed that the prognostic capabilities of each model at 3, 5, and 8 years were all greater than 0.7, and the final prognostic capabilities of the models were all greater than 0.9. By reviewing other databases and utilizing qPCR, we verified the established THCA gene model. In addition, gene set enrichment analysis showed that abnormal AS events might play key roles in tumor development and progression of THCA by participating in changes in molecular structure, homeostasis of the cell environment and in cell energy. Finally, a splicing correlation network was established to reveal the potential regulatory patterns between the predicted splicing factors and AS event candidates. In summary, AS should be considered an important prognostic indicator of THCA. Our results will help to elucidate the underlying mechanism of AS in the process of THCA tumorigenesis and broaden the prognostic and clinical application of molecular targeted therapy for THCA.
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Affiliation(s)
- Baoai Han
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minlan Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiuping Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengzhi Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiang Xie
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guorun Fan
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Davood K Hosseini
- Department of Internal Medicine, Hackensack University Medical Center, Hackensack, NJ, United States
| | - Jintao Yu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Song
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiong Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Haiying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Gelatinous bone marrow transformation and emergence of clonal Philadelphia-negative cytogenetic abnormalities with excess blasts in a patient with chronic myeloid leukemia treated with dasatinib. Anticancer Drugs 2019; 30:416-421. [DOI: 10.1097/cad.0000000000000763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Role of pseudoexons and pseudointrons in human cancer. Int J Cell Biol 2013; 2013:810572. [PMID: 24204383 PMCID: PMC3800588 DOI: 10.1155/2013/810572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/09/2013] [Indexed: 11/18/2022] Open
Abstract
In all eukaryotic organisms, pre-mRNA splicing and alternative splicing processes play an essential role in regulating the flow of information required to drive complex developmental and metabolic pathways. As a result, eukaryotic cells have developed a very efficient macromolecular machinery, called the spliceosome, to correctly recognize the pre-mRNA sequences that need to be inserted in a mature mRNA (exons) from those that should be removed (introns). In healthy individuals, alternative and constitutive splicing processes function with a high degree of precision and fidelity in order to ensure the correct working of this machinery. In recent years, however, medical research has shown that alterations at the splicing level play an increasingly important role in many human hereditary diseases, neurodegenerative processes, and especially in cancer origin and progression. In this minireview, we will focus on several genes whose association with cancer has been well established in previous studies, such as ATM, BRCA1/A2, and NF1. In particular, our objective will be to provide an overview of the known mechanisms underlying activation/repression of pseudoexons and pseudointrons; the possible utilization of these events as biomarkers of tumor staging/grading; and finally, the treatment options for reversing pathologic splicing events.
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Gniot M, Wasilewska EM, Lewandowski K. K356dup--an in-frame insertion in the BCR-ABL gene in an imatinib-resistant chronic myeloid leukemia. Int J Lab Hematol 2012; 34:e3-6. [PMID: 25998099 DOI: 10.1111/j.1751-553x.2012.01443.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M Gniot
- Department of Hematology, University of Medical Sciences, Poznan, Poland.
| | - E M Wasilewska
- Department of Hematology, University of Medical Sciences, Bialystok, Poland
| | - K Lewandowski
- Department of Hematology, University of Medical Sciences, Poznan, Poland
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5
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Alikian M, Gerrard G, Subramanian PG, Mudge K, Foskett P, Khorashad JS, Lim AC, Marin D, Milojkovic D, Reid A, Rezvani K, Goldman J, Apperley J, Foroni L. BCR-ABL1 kinase domain mutations: methodology and clinical evaluation. Am J Hematol 2012; 87:298-304. [PMID: 22231203 DOI: 10.1002/ajh.22272] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 11/24/2011] [Accepted: 12/01/2011] [Indexed: 12/31/2022]
Abstract
The introduction of tyrosine kinase inhibitors (TKIs), starting with imatinib and followed by second and third generation TKIs, has significantly changed the clinical management of patients with chronic myeloid leukemia (CML). Despite their unprecedented clinical success, a proportion of patients fail to achieve complete cytogenetic remission by 12 months of treatment (primary resistance) while others experience progressive resistance after an initial response (secondary resistance). BCR-ABL1 kinase domain (KD) mutations have been detected in a proportion of patients at the time of treatment failure, and therefore their identification and monitoring plays an important role in therapeutic decisions particularly when switching TKIs. When monitoring KD mutations in a clinical laboratory, the choice of method should take into account turnaround time, cost, sensitivity, specificity, and ability to accurately quantify the size of the mutant clone. In this article, we describe in a "manual" style the methods most widely used in our laboratory to monitor KD mutations in patients with CML including direct sequencing, D-HPLC, and pyrosequencing. Advantages, disadvantages, interpretation of results, and their clinical applications are reviewed for each method.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Chromatography, High Pressure Liquid/methods
- DNA Mutational Analysis/methods
- Drug Resistance, Neoplasm/genetics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Genes, abl
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mutation
- Polymerase Chain Reaction/methods
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Protein Structure, Tertiary/genetics
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Quality Control
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Sequence Analysis, DNA/methods
- Specimen Handling
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Affiliation(s)
- Mary Alikian
- Imperial Molecular Pathology Laboratory, Imperial College NHS Trust and Academic Science Centre, Hammersmith Hospital, London W12 OHS, United Kingdom
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6
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Alternative splicing in oncogenic kinases: from physiological functions to cancer. J Nucleic Acids 2011; 2012:639062. [PMID: 22007291 PMCID: PMC3189609 DOI: 10.1155/2012/639062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/14/2011] [Indexed: 01/13/2023] Open
Abstract
Among the 518 protein kinases encoded by the human kinome, several of them act as oncoproteins in human cancers. Like other eukaryotic genes, oncogenes encoding protein kinases are frequently subjected to alternative splicing in coding as well as noncoding sequences. In the present paper, we will illustrate how alternative splicing can significantly impact on the physiological functions of oncogenic protein kinases, as demonstrated by mouse genetic model studies. This includes examples of membrane-bound tyrosine kinases receptors (FGFR2, Ret, TrkB, ErbB4, and VEGFR) as well as cytosolic protein kinases (B-Raf). We will further discuss how regular alternative splicing events of these kinases are in some instances implicated in oncogenic processes during tumor progression (FGFR, TrkB, ErbB2, Abl, and AuroraA). Finally, we will present typical examples of aberrant splicing responsible for the deregulation of oncogenic kinases activity in cancers (AuroraB, Jak2, Kit, Met, and Ron).
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8
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Branford S, Hughes TP. Practical Considerations for Monitoring Patients With Chronic Myeloid Leukemia. Semin Hematol 2010; 47:327-34. [DOI: 10.1053/j.seminhematol.2010.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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ABL Alternative Splicing Is Quite Frequent in Normal Population - Letter. Mol Cancer Ther 2010; 9:772; author reply 772. [DOI: 10.1158/1535-7163.mct-09-0078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Lee TS, Ma W, Zhang X, Albitar M, Giles F, Cortes J, Kantarjian H. BCR-ABL1INS35 Is Not Uncommon in CML Patients and Is Related to Resistance and Sensitivity to Inhibitors in CML Treatment - Response. Mol Cancer Ther 2010. [DOI: 10.1158/1535-7163.mct-09-1116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Tai-Sung Lee
- Biomedical Informatics and Computational Biology, and Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Wanlong Ma
- Department of Hematopathology, Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Xi Zhang
- Department of Hematopathology, Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Maher Albitar
- Department of Hematopathology, Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Francis Giles
- Division of Hematology, Cancer Therapy and Research Center, University of Texas, Health Science Center, San Antonio, Texas
| | - Jorge Cortes
- Department of Leukemia, M.D. Anderson Cancer Center, University of Texas, Houston, Texas
| | - Hagop Kantarjian
- Department of Leukemia, M.D. Anderson Cancer Center, University of Texas, Houston, Texas
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11
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Jones D, Kamel-Reid S, Bahler D, Dong H, Elenitoba-Johnson K, Press R, Quigley N, Rothberg P, Sabath D, Viswanatha D, Weck K, Zehnder J. Laboratory practice guidelines for detecting and reporting BCR-ABL drug resistance mutations in chronic myelogenous leukemia and acute lymphoblastic leukemia: a report of the Association for Molecular Pathology. J Mol Diagn 2008; 11:4-11. [PMID: 19095773 DOI: 10.2353/jmoldx.2009.080095] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The BCR-ABL tyrosine kinase produced by the t(9;22)(q34;q11) translocation, also known as the Philadelphia chromosome, is the initiating event in chronic myeloid leukemia (CML) and Ph+ acute lymphoblastic leukemia (ALL). Targeting of BCR-ABL with tyrosine kinase inhibitors (TKIs) has resulted in rapid clinical responses in the vast majority of patients with CML and Philadelphia chromosome+ ALL. However, long-term use of TKIs occasionally results in emergence of therapy resistance, in part through the selection of clones with mutations in the BCR-ABL kinase domain. We present here an overview of the current practice in monitoring for such mutations, including the methods used, the clinical and laboratory criteria for triggering mutational analysis, and the guidelines for reporting BCR-ABL mutations. We also present a proposal for a public database for correlating mutational status with in vitro and in vivo responses to different TKIs to aid in the interpretation of mutation studies.
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Affiliation(s)
- Dan Jones
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; University of Texas M. D. Anderson Cancer Center, Houston, Texas.
| | - Suzanne Kamel-Reid
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; The University Health Network, Toronto, Canada
| | - David Bahler
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; ARUP Laboratories, Salt Lake City, Utah
| | - Henry Dong
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; Genzyme Genetics, New York City, New York
| | - Kojo Elenitoba-Johnson
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; University of Michigan Medical School, Ann Arbor, Michigan
| | - Richard Press
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; Oregon Health & Science University, Portland, Oregon
| | - Neil Quigley
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; Molecular Pathology Laboratory Network, Inc., Maryville, Tennessee
| | - Paul Rothberg
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; University of Rochester Medical Center, Rochester, New York
| | - Dan Sabath
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; University of Washington, Seattle, Washington
| | - David Viswanatha
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; Mayo Clinic, Rochester, Minnesota
| | - Karen Weck
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; University of North Carolina, Chapel Hill, North Carolina
| | - James Zehnder
- ABL Mutation Working Group of the Association for Molecular Pathology, Clinical Practice Committee, Houston, Texas; Stanford University, Stanford, California
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