1
|
Mochimaru Y, Yoshida K. Functional Roles of DYRK2 as a Tumor Regulator. Curr Issues Mol Biol 2023; 45:8539-8551. [PMID: 37886981 PMCID: PMC10605165 DOI: 10.3390/cimb45100538] [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: 10/10/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023] Open
Abstract
The dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) regulates the induction of apoptosis and DNA repair, metastasis inhibition, cell cycle G1/S transition, protein scaffold stability for E3 ligase complexes, and embryogenesis. Owing to these functions, DYRK2 is thought to regulate tumorigenesis, and its function in cancer has been investigated. Notably, DYRK2 has been reported to function as a tumor suppressor; however, it has also been reported to act as an oncogene in some cancers. This discrepancy makes it difficult to elucidate the conserved functions of DYRK2 in cancer. Here, we reviewed the functions of DYRK2 in various cancers. Patient tissue samples were evaluated for each cancer type. Although some studies have used cell lines and/or xenografts to elucidate the mechanism of DYRK2 function, these studies are not sufficient to understand the role of DYRK2 in cancers. In particular, studies using genetically modified mice would help us to understand the reported functional duality of DYRK2 in cancer.
Collapse
Affiliation(s)
| | - Kiyotsugu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo 105-8461, Japan;
| |
Collapse
|
2
|
D’Antona L, Amato R, Brescia C, Rocca V, Colao E, Iuliano R, Blazer-Yost BL, Perrotti N. Kinase Inhibitors in Genetic Diseases. Int J Mol Sci 2023; 24:ijms24065276. [PMID: 36982349 PMCID: PMC10048847 DOI: 10.3390/ijms24065276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Over the years, several studies have shown that kinase-regulated signaling pathways are involved in the development of rare genetic diseases. The study of the mechanisms underlying the onset of these diseases has opened a possible way for the development of targeted therapies using particular kinase inhibitors. Some of these are currently used to treat other diseases, such as cancer. This review aims to describe the possibilities of using kinase inhibitors in genetic pathologies such as tuberous sclerosis, RASopathies, and ciliopathies, describing the various pathways involved and the possible targets already identified or currently under study.
Collapse
Affiliation(s)
- Lucia D’Antona
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Rosario Amato
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Carolina Brescia
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
| | - Valentina Rocca
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
- Department of Experimental and Clinical Medicine, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
| | - Emma Colao
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
| | - Bonnie L. Blazer-Yost
- Department of Biology, Indiana University Purdue University, Indianapolis, IN 46202, USA
| | - Nicola Perrotti
- Department of Health Sciences, University “Magna Graecia” at Catanzaro, 88100 Catanzaro, Italy
- Medical Genetics Unit, University Hospital “Mater Domini” at Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
| |
Collapse
|
3
|
Cicek M, Unsal V, Emre A, Doganer A. Investigation of the Effects of Apigenin, a Possible Therapeutic Agent, on Cytotoxic and SWH Pathway in Colorectal Cancer (HT29) Cells. Adv Pharm Bull 2023; 13:188-195. [PMID: 36721804 PMCID: PMC9871274 DOI: 10.34172/apb.2023.020] [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: 07/01/2020] [Revised: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 02/03/2023] Open
Abstract
Purpose: Colorectal cancer (CRC) is one of the most common and fatal malignancies in humans, still leading to serious morbidity and mortality. We here aimed to investigate the effects of flavonoid apigenin, which is considered to have anti-tumoral activity on CRC with high epidemiological prevalence, on cell proliferation and cell survivals, and the positive and negative dose-dependent effects of genetic or mutational alterations in SWH pathway components on HT29 CRC cell lines. Methods: Human colon cancer cell lines HT-29 were commercially available. In each flask, 5 groups were formed, each of which consists of 5,000 cells for different dose groups and the cells were plated. After a 24 and 48 h incubation period, cytotoxicity values were measured by MTT assay and gene expression was assessed by real-time polymerase chain reaction (PCR) analysis method. Results: Application of 12.5 and 25 nM of apigenin significantly increased cell death in HT29 cell lines. LATS1, STK3 and TP53 gene expression decreased in the same dose groups compared to control and other groups. Conclusion: It has been concluded that TP53 gene is strongly correlated with LATS1 and STK3 genes among the SWH pathway factors in the progression of CRC and could be used as an important marker for early detection of malignant transmission. In addition, it may be effective in CRC cases especially when 25 nM of apigenin applies for therapeutic purpose.
Collapse
Affiliation(s)
- Mustafa Cicek
- Department of Medical Biology, Faculty of Medicine, Kahramanmaras Sutcu Imam University, Kahramanmaraş, Turkey
| | - Velid Unsal
- Department of Nutrition and Dietetics, Faculty of Health Science, Mardin Artuklu University, 47200, Mardin, Turkey.,Corresponding Author: Velid Unsal, Tel: (0482) 2134002,
| | - Arif Emre
- Department of Surgery, Kahramanmaras Sutcu Imam University Faculty of Medicine, 46100, Kahramanmaras, Turkey
| | - Adem Doganer
- Department of Biostatistics and Medical Informatics, Kahramanmaras Sutcu Imam University Faculty of Medicine, 46100, Kahramanmaras, Turkey
| |
Collapse
|
4
|
Rodriguez M, Kannangara A, Chlebowicz J, Akella R, He H, Tambar UK, Goldsmith EJ. Synthesis and Structural Characterization of Novel Trihalo-sulfone Inhibitors of WNK1. ACS Med Chem Lett 2022; 13:1678-1684. [PMID: 36262391 PMCID: PMC9575160 DOI: 10.1021/acsmedchemlett.2c00216] [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: 05/09/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
With No lysine (K) [WNK] kinases are structurally unique serine/threonine protein kinases that have therapeutic potential for blood pressure regulation and cancer. A novel class of trihalo-sulfone compounds was identified by high-throughput screening. Trihalo-sulfone 1 emerged as an effective inhibitor of WNK1 with an IC50 value of 1.6 μM. Herein, we define chemical features necessary for inhibition of WNK1 using chemical synthesis and X-ray crystallography. Analogues that probed the role of specific functional groups to the inhibitory activity were synthesized. X-ray structures of trihalo-sulfone 1 and a second trihalo-sulfone 23 bound to WNK1 revealed active site binding to two of the three previously defined canonical inhibitor binding pockets as well as a novel binding site for the trihalo-sulfone moiety. The elucidation of these novel interaction sites may allow for the strategic design of even more selective and potent WNK inhibitors.
Collapse
Affiliation(s)
- Melanie Rodriguez
- Department
of Biochemistry, The University of Texas
Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Ashari Kannangara
- Department
of Biophysics, The University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, United States
| | - Julita Chlebowicz
- Department
of Biophysics, The University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, United States
| | - Radha Akella
- Department
of Biophysics, The University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, United States
| | - Haixia He
- Department
of Biophysics, The University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, United States
| | - Uttam K. Tambar
- Department
of Biochemistry, The University of Texas
Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Elizabeth J. Goldsmith
- Department
of Biophysics, The University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, United States
| |
Collapse
|
5
|
Petljak M, Dananberg A, Chu K, Bergstrom EN, Striepen J, von Morgen P, Chen Y, Shah H, Sale JE, Alexandrov LB, Stratton MR, Maciejowski J. Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature 2022; 607:799-807. [PMID: 35859169 PMCID: PMC9329121 DOI: 10.1038/s41586-022-04972-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/13/2022] [Indexed: 02/07/2023]
Abstract
The APOBEC3 family of cytosine deaminases has been implicated in some of the most prevalent mutational signatures in cancer1-3. However, a causal link between endogenous APOBEC3 enzymes and mutational signatures in human cancer genomes has not been established, leaving the mechanisms of APOBEC3 mutagenesis poorly understood. Here, to investigate the mechanisms of APOBEC3 mutagenesis, we deleted implicated genes from human cancer cell lines that naturally generate APOBEC3-associated mutational signatures over time4. Analysis of non-clustered and clustered signatures across whole-genome sequences from 251 breast, bladder and lymphoma cancer cell line clones revealed that APOBEC3A deletion diminished APOBEC3-associated mutational signatures. Deletion of both APOBEC3A and APOBEC3B further decreased APOBEC3 mutation burdens, without eliminating them. Deletion of APOBEC3B increased APOBEC3A protein levels, activity and APOBEC3A-mediated mutagenesis in some cell lines. The uracil glycosylase UNG was required for APOBEC3-mediated transversions, whereas the loss of the translesion polymerase REV1 decreased overall mutation burdens. Together, these data represent direct evidence that endogenous APOBEC3 deaminases generate prevalent mutational signatures in human cancer cells. Our results identify APOBEC3A as the main driver of these mutations, indicate that APOBEC3B can restrain APOBEC3A-dependent mutagenesis while contributing its own smaller mutation burdens and dissect mechanisms that translate APOBEC3 activities into distinct mutational signatures.
Collapse
Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevan Chu
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Patrick von Morgen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyang Chen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hina Shah
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK.
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
6
|
Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants. Cancers (Basel) 2021; 13:cancers13205034. [PMID: 34680183 PMCID: PMC8534219 DOI: 10.3390/cancers13205034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/14/2021] [Accepted: 10/01/2021] [Indexed: 12/14/2022] Open
Abstract
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.
Collapse
|
7
|
Kan Y, Jiang L, Tang J, Guo Y, Guo F. A systematic view of computational methods for identifying driver genes based on somatic mutation data. Brief Funct Genomics 2021; 20:333-343. [PMID: 34312663 DOI: 10.1093/bfgp/elab032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Abnormal changes of driver genes are serious for human health and biomedical research. Identifying driver genes, exactly from enormous genes with mutations, promotes accurate diagnosis and treatment of cancer. A lot of works about uncovering driver genes have been developed over the past decades. By analyzing previous works, we find that computational methods are more efficient than traditional biological experiments when distinguishing driver genes from massive data. In this study, we summarize eight common computational algorithms only using somatic mutation data. We first group these methods into three categories according to mutation features they apply. Then, we conclude a general process of nominating candidate cancer driver genes. Finally, we evaluate three representative methods on 10 kinds of cancer derived from The Cancer Genome Atlas Program and five Chinese projects from the International Cancer Genome Consortium. In addition, we compare results of methods with various parameters. Evaluation is performed from four perspectives, including CGC, OG/TSG, Q-value and QQQuantile-Quantileplot. To sum up, we present algorithms using somatic mutation data in order to offer a systematic view of various mutation features and lay the foundation of methods based on integration of mutation information and other types of data.
Collapse
Affiliation(s)
- Yingxin Kan
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Limin Jiang
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,School of Computational Science and Engineering, University of South Carolina, Columbia, U.S
| | - Yan Guo
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, U.S
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha, China
| |
Collapse
|
8
|
Krasny L, Huang PH. Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology. Mol Omics 2020; 17:29-42. [PMID: 33034323 DOI: 10.1039/d0mo00072h] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Data-independent acquisition mass spectrometry (DIA-MS) is a next generation proteomic methodology that generates permanent digital proteome maps offering highly reproducible retrospective analysis of cellular and tissue specimens. The adoption of this technology has ushered a new wave of oncology studies across a wide range of applications including its use in molecular classification, oncogenic pathway analysis, drug and biomarker discovery and unravelling mechanisms of therapy response and resistance. In this review, we provide an overview of the experimental workflows commonly used in DIA-MS, including its current strengths and limitations versus conventional data-dependent acquisition mass spectrometry (DDA-MS). We further summarise a number of key studies to illustrate the power of this technology when applied to different facets of oncology. Finally we offer a perspective of the latest innovations in DIA-MS technology and machine learning-based algorithms necessary for driving the development of high-throughput, in-depth and reproducible proteomic assays that are compatible with clinical diagnostic workflows, which will ultimately enable the delivery of precision cancer medicine to achieve optimal patient outcomes.
Collapse
Affiliation(s)
- Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | | |
Collapse
|
9
|
Martínez-Jiménez F, Muiños F, Sentís I, Deu-Pons J, Reyes-Salazar I, Arnedo-Pac C, Mularoni L, Pich O, Bonet J, Kranas H, Gonzalez-Perez A, Lopez-Bigas N. A compendium of mutational cancer driver genes. Nat Rev Cancer 2020; 20:555-572. [PMID: 32778778 DOI: 10.1038/s41568-020-0290-x] [Citation(s) in RCA: 534] [Impact Index Per Article: 133.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
A fundamental goal in cancer research is to understand the mechanisms of cell transformation. This is key to developing more efficient cancer detection methods and therapeutic approaches. One milestone towards this objective is the identification of all the genes with mutations capable of driving tumours. Since the 1970s, the list of cancer genes has been growing steadily. Because cancer driver genes are under positive selection in tumorigenesis, their observed patterns of somatic mutations across tumours in a cohort deviate from those expected from neutral mutagenesis. These deviations, which constitute signals of positive selection, may be detected by carefully designed bioinformatics methods, which have become the state of the art in the identification of driver genes. A systematic approach combining several of these signals could lead to a compendium of mutational cancer genes. In this Review, we present the Integrative OncoGenomics (IntOGen) pipeline, an implementation of such an approach to obtain the compendium of mutational cancer drivers. Its application to somatic mutations of more than 28,000 tumours of 66 cancer types reveals 568 cancer genes and points towards their mechanisms of tumorigenesis. The application of this approach to the ever-growing datasets of somatic tumour mutations will support the continuous refinement of our knowledge of the genetic basis of cancer.
Collapse
Affiliation(s)
- Francisco Martínez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Deu-Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Iker Reyes-Salazar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jose Bonet
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hanna Kranas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
| |
Collapse
|
10
|
Mehnert M, Ciuffa R, Frommelt F, Uliana F, van Drogen A, Ruminski K, Gstaiger M, Aebersold R. Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Nat Commun 2020; 11:3563. [PMID: 32678104 PMCID: PMC7366679 DOI: 10.1038/s41467-020-17387-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/26/2020] [Indexed: 01/09/2023] Open
Abstract
Rapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.
Collapse
Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Kilian Ruminski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
11
|
Velazquez AI, McCoach CE. Tumor evolution in epidermal growth factor receptor mutated non-small cell lung cancer. J Thorac Dis 2020; 12:2896-2909. [PMID: 32642202 PMCID: PMC7330358 DOI: 10.21037/jtd.2019.08.31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
As the incidence of cancer increases worldwide there is an unmet need to understand cancer evolution to improve patient outcomes. Our growing knowledge of cancer cells' clonal expansion, heterogeneity, adaptation, and relationships within the tumor immune compartment and with the tumor microenvironment has made clear that cancer is a disease that benefits from heterogeneity and evolution. This review outlines recent knowledge of non-small cell lung cancer (NSCLC) pathogenesis and tumor progression from an evolutionary standpoint, focused on the role of oncogenic driver mutations as epidermal growth factor receptor (EGFR). Understanding lung cancer evolution during tumor development, growth, and under treatment pressures is crucial to improve therapeutic interventions and patient outcomes.
Collapse
Affiliation(s)
- Ana I. Velazquez
- Department of Medicine, Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Caroline E. McCoach
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| |
Collapse
|
12
|
Somatic mutations in the DNA repairome in prostate cancers in African Americans and Caucasians. Oncogene 2020; 39:4299-4311. [PMID: 32300177 PMCID: PMC7239769 DOI: 10.1038/s41388-020-1280-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022]
Abstract
Most hereditary tumors show aberrations in DNA repair genes or their regulators. In contrast, only a minority of sporadic tumors show alterations in these genes. As a result, genomic instability is currently considered an enhancer of tumorigenesis rather than an obligatory event in this process. However, tumor heterogeneity presents a significant technical challenge for most cancer genomics studies performed at less than 100× mean resolution depth. To address the importance of genomic instability in prostate carcinogenesis and tumor progression, we performed ultrahigh depth exome sequencing of 124 DNA damage repair/response (repairome) genes in 63 tumors and matched normal tissue samples in African Americans and Caucasians. The average sequence depth was 712-fold for DNA isolated from normal tissue and 368-fold for FFPE tumors. We identified 671 somatic mutations in tumors from African Americans and 762 somatic mutations in tumors in Caucasians. The most frequently mutated DNA repairome genes were EXO1, ATR, POLQ, NEIL3, ERCC6, BRCA2, BRCA1, XPC, JAG1, RPA1, POLE, ATM, and LIG1 in African American men, and POLQ, NEIL3, POLB, BRCA2, EXO1, ERCC6, ATR, RBBP8, BRCA1, ATM, JAG1, XPC, and POLE in Caucasians. We found that 89% of tumors had at least one mutation in nucleotide excision repair pathway genes in African Americans, whereas >40% of tumors had mutations in base excision repair pathway genes in Caucasians. We further identified a marginal increase in mutation rate in tumors in African Americans with increasing age. Tumors in Caucasians did not show a correlation with age, but a progressive increase in the mutation rate was observed at higher Gleason scores. Our data reveal significant differences in the molecular signatures in the DNA repairome in prostate cancer between African Americans and Caucasians. These data also have substantial implications regarding the well-known health disparities in prostate cancer, such as the higher mortality in African Americans than Caucasians.
Collapse
|
13
|
Germline APOBEC3B deletion influences clinicopathological parameters in luminal-A breast cancer: evidences from a southern Brazilian cohort. J Cancer Res Clin Oncol 2020; 146:1523-1532. [PMID: 32285256 DOI: 10.1007/s00432-020-03208-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE APOBEC3A and APOBEC3B cytidine deaminases have been implicated in the pathogenesis of multiple cancers, including breast cancer (BC). A germline deletion linking APOBEC3A and APOBEC3B loci (A3A/B) has been associated with higher APOBEC-mediated mutational burden, but its association with BC risk have been controversial. Therefore, this study investigated the association between A3A/B and BC susceptibility and clinical presentation in a Brazilian cohort. METHODS A3A/B deletion was evaluated through allele-specific PCR in 341 BC patients and 397 women without familial or personal history of neoplasia from Brazil and associations with susceptibility to BC subtypes were tested through age-adjusted logistic models while correlations with clinicopathological parameters were tested using Kendall's tests. RESULTS No association was found between A3A/B and BC susceptibility; however, in Luminal-A BCs, it was positively correlated with tumor size (Tau-c = 0.125) and Ki67 (Tau-c = 0.116) and negatively correlated with lymph node metastasis (LNM) (Tau-c = - 0.162). The negative association between A3A/B with LNM in Luminal-A BCs remained significant even after adjusting for tumor size and Ki67 in logistic models (OR = 0.22; p = 0.008). CONCLUSION These results show that although A3A/B may not modify BC susceptibility in Brazilian population, it may affect clinicopathological features in BC subtypes, promoting tumor cell proliferation while being negatively associated with LNM in Luminal-A BCs.
Collapse
|
14
|
Active targeted ligand-aza-BODIPY conjugate for near-infrared photodynamic therapy in melanoma. Int J Pharm 2020; 579:119189. [DOI: 10.1016/j.ijpharm.2020.119189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/11/2020] [Accepted: 02/28/2020] [Indexed: 01/02/2023]
|
15
|
Mannakee BK, Gutenkunst RN. BATCAVE: calling somatic mutations with a tumor- and site-specific prior. NAR Genom Bioinform 2020; 2:lqaa004. [PMID: 32051931 PMCID: PMC7003682 DOI: 10.1093/nargab/lqaa004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 02/06/2023] Open
Abstract
Detecting somatic mutations withins tumors is key to understanding treatment resistance, patient prognosis and tumor evolution. Mutations at low allelic frequency, those present in only a small portion of tumor cells, are particularly difficult to detect. Many algorithms have been developed to detect such mutations, but none models a key aspect of tumor biology. Namely, every tumor has its own profile of mutation types that it tends to generate. We present BATCAVE (Bayesian Analysis Tools for Context-Aware Variant Evaluation), an algorithm that first learns the individual tumor mutational profile and mutation rate then uses them in a prior for evaluating potential mutations. We also present an R implementation of the algorithm, built on the popular caller MuTect. Using simulations, we show that adding the BATCAVE algorithm to MuTect improves variant detection. It also improves the calibration of posterior probabilities, enabling more principled tradeoff between precision and recall. We also show that BATCAVE performs well on real data. Our implementation is computationally inexpensive and straightforward to incorporate into existing MuTect pipelines. More broadly, the algorithm can be added to other variant callers, and it can be extended to include additional biological features that affect mutation generation.
Collapse
Affiliation(s)
- Brian K Mannakee
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
16
|
Roles of TrkC Signaling in the Regulation of Tumorigenicity and Metastasis of Cancer. Cancers (Basel) 2020; 12:cancers12010147. [PMID: 31936239 PMCID: PMC7016819 DOI: 10.3390/cancers12010147] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
Tropomyosin receptor kinase (Trk) C contributes to the clinicopathology of a variety of human cancers, and new chimeric oncoproteins containing the tyrosine kinase domain of TrkC occur after fusion to the partner genes. Overexpression of TrkC and TrkC fusion proteins was observed in patients with a variety of cancers, including mesenchymal, hematopoietic, and those of epithelial cell lineage. Both microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) were involved in the regulation of TrkC expression through transcriptional and posttranscriptional alteration. Aberrant activation of TrkC and TrkC fusion proteins markedly induces the epithelial-mesenchymal transition (EMT) program, growth rate, tumorigenic capacity via constitutive activation of Ras-MAP kinase (MAPK), PI3K-AKT, and the JAK2-STAT3 pathway. The clinical trial of TrkC or TrkC fusion-positive cancers with newly developed Trk inhibitors demonstrated that Trk inhibitors were highly effective in inducing tumor regression in patients who do not harbor mutations in the kinase domain. Recently, there has been a progressive accumulation of mutations in TrkC or the TrkC fusion protein detected in the clinic and its related cancer cell lines caused by high-throughput DNA sequencing. Despite given the high overall response rate against Trk or Trk fusion proteins-positive solid tumors, acquired drug resistance was observed in patients with various cancers caused by mutations in the Trk kinase domain. To overcome acquired resistance caused by kinase domain mutation, next-generation Trk inhibitors have been developed, and these inhibitors are currently under investigation in clinical trials.
Collapse
|
17
|
Hashemi M, Moazeni-Roodi A, Taheri M. Association of APOBEC3 deletion with cancer risk: A meta-analysis of 26 225 cases and 37 201 controls. Asia Pac J Clin Oncol 2019; 15:275-287. [PMID: 30693645 DOI: 10.1111/ajco.13107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/27/2018] [Indexed: 12/11/2022]
Abstract
Previous studies have found inconsistent results regarding gene deletion in APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) and risk of cancer. We conducted a meta-analysis of all eligible case-control studies to find out the associations between APOBEC3 deletion and cancer risk by pooling the odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Overall, the findings from 20 studies (13 articles) involving of a total of 26 225 cases and 37 201 controls revealed that DD genotype was associated significantly with increased cancer risk compared to II genotype (OR = 1.25, 95% CI = 1.01-1.56, P = 0.04). Stratified analysis from 10 studies including 14 757 cases and 17 930 controls revealed that I/D variant significantly increased the risk of breast cancer in heterozygous codominant (OR = 1.15, 95% CI = 1.03-1.28, P = 0.02, ID vs II), dominant (OR = 1.15, 95% CI = 1.01-1.31, P = 0.03, ID + DD vs II), overdominant (OR = 1.11, 95% CI = 1.05-1.25, P < 0.0001, ID vs DD + II) and allele (OR = 1.15, 95% CI = 1.13-1.25, P = 0.03, D vs I) inheritance models. In conclusion, the data propose that APOBEC3 deletion is significantly associated with increased susceptibility to cancer in overall and breast cancer. Our findings require well-designed replication in a larger independent genetic association study with larger sample sizes in diverse ethnicities.
Collapse
Affiliation(s)
- Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Abdolkarim Moazeni-Roodi
- Department of Clinical Biochemistry, School of Medicine, Iranshahr University of Medical Sciences, Iranshahr, Iran
| | - Mohsen Taheri
- Department of Genetics, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| |
Collapse
|
18
|
Agajanian S, Oluyemi O, Verkhivker GM. Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations. Front Mol Biosci 2019; 6:44. [PMID: 31245384 PMCID: PMC6579812 DOI: 10.3389/fmolb.2019.00044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to preprocess the DNA information. These classifiers were benchmarked against their tree-based alternatives in order to evaluate the performance on a relative scale. We then integrated DNA-based scores generated by CNN with various categories of conservational, evolutionary and functional features into a generalized random forest classifier. The results of this study have demonstrated that CNN can learn high level features from genomic information that are complementary to the ensemble-based predictors often employed for classification of cancer mutations. By combining deep learning-generated score with only two main ensemble-based functional features, we can achieve a superior performance of various machine learning classifiers. Our findings have also suggested that synergy of nucleotide-based deep learning scores and integrated metrics derived from protein sequence conservation scores can allow for robust classification of cancer driver mutations with a limited number of highly informative features. Machine learning predictions are leveraged in molecular simulations, protein stability, and network-based analysis of cancer mutations in the protein kinase genes to obtain insights about molecular signatures of driver mutations and enhance the interpretability of cancer-specific classification models.
Collapse
Affiliation(s)
- Steve Agajanian
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
| |
Collapse
|
19
|
McCoach CE, Bivona TG. Engineering Multidimensional Evolutionary Forces to Combat Cancer. Cancer Discov 2019; 9:587-604. [PMID: 30992280 PMCID: PMC6497542 DOI: 10.1158/2159-8290.cd-18-1196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/28/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
With advances in technology and bioinformatics, we are now positioned to view and manage cancer through an evolutionary lens. This perspective is critical as our appreciation for the role of tumor heterogeneity, tumor immune compartment, and tumor microenvironment on cancer pathogenesis and evolution grows. Here, we explore recent knowledge on the evolutionary basis of cancer pathogenesis and progression, viewing tumors as multilineage, multicomponent organisms whose growth is regulated by subcomponent fitness relationships. We propose reconsidering some current tenets of the cancer management paradigm in order to take better advantage of crucial fitness relationships to improve outcomes of patients with cancer. SIGNIFICANCE: Tumor and tumor immune compartment and microenvironment heterogeneity, and their evolution, are critical disease features that affect treatment response. The impact and interplay of these components during treatment are viable targets to improve clinical response. In this article, we consider how tumor cells, the tumor immune compartment and microenvironment, and epigenetic factors interact and also evolve during treatment. We evaluate the convergence of these factors and suggest innovative treatment concepts that leverage evolutionary relationships to limit tumor growth and drug resistance.
Collapse
Affiliation(s)
- Caroline E McCoach
- Department of Medicine, University of California, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
| |
Collapse
|
20
|
Stein MK, Morris LK, Martin MG. Next-Generation Sequencing Identifies Novel RTK VUSs in Breast Cancer with an Emphasis on ROS1, ERBB4, ALK and NTRK3. Pathol Oncol Res 2018; 26:593-595. [PMID: 30460540 DOI: 10.1007/s12253-018-0550-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 11/16/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Matthew K Stein
- West Cancer Center, Memphis, TN, USA. .,University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Lindsay K Morris
- College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | | |
Collapse
|
21
|
Chen X, Lu B, Ma Q, Ji CD, Li JZ. EphA3 inhibits migration and invasion of esophageal cancer cells by activating the mesenchymal‑epithelial transition process. Int J Oncol 2018; 54:722-732. [PMID: 30483759 DOI: 10.3892/ijo.2018.4639] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 11/02/2018] [Indexed: 11/06/2022] Open
Abstract
Eph receptor tyrosine kinases are critical for cell‑cell communication during normal and oncogenic development. Eph receptor A3 (EphA3) expression is associated with tumor promotion in certain types of cancer; however, it acts as a tumor suppressor in others. The expression levels of EphA3 and its effects on tumor progression in esophageal squamous cell carcinoma (ESCC) cell lines were determined using reverse transcription‑quantitative polymerase chain reaction analysis and a Transwell invasion assay. The present study demonstrated that EphA3 expression was decreased in ESCC tissues and cell lines. Treatment with the DNA methylation inhibitor 5‑aza‑2'‑deoxycytidine increased the mRNA expression levels of EphA3 in the ESCC cell lines KYSE510 and KYSE30. In addition, overexpression of EphA3 in KYSE450 and KYSE510 cells inhibited cell migration and invasion. EphA3 overexpression also decreased RhoA GTPase. Furthermore, EphA3 overexpression induced mesenchymal‑epithelial transition, as demonstrated by epithelial‑like morphological alterations, increased expression of epithelial proteins (E‑cadherin and the tight junction protein 1 zonula occludens‑1) and decreased expression of mesenchymal proteins (Vimentin, N‑cadherin and Snail). Conversely, silencing EphA3 in KYSE410 cells triggered epithelial‑mesenchymal transition, and promoted cell migration and invasion. These results suggested that EphA3 may serve a tumor‑suppressor role in ESCC.
Collapse
Affiliation(s)
- Xia Chen
- Key Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, P.R. China
| | - Bin Lu
- International Joint Cancer Institute, Second Military Medical University, Shanghai 200433, P.R. China
| | - Qian Ma
- International Joint Cancer Institute, Second Military Medical University, Shanghai 200433, P.R. China
| | - Cheng-Dong Ji
- Department of Scientific Research Management, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, P.R. China
| | - Jian-Zhong Li
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai 200433, P.R. China
| |
Collapse
|
22
|
Zhang Z, Li Z, Chen W. Down-regulated G protein-coupled receptor kinase 6 leads to apoptosis in multiple myeloma MM1R cells. Exp Ther Med 2018; 16:4253-4259. [PMID: 30402162 DOI: 10.3892/etm.2018.6722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptor kinase 6 (GRK6) is highly expressed in multiple myeloma (MM) cell lines, but absent or only weakly expressed in most primary human somatic cells. In the present study, GRK6 expression was assessed in MM patients and healthy individuals by quantitative polymerase chain reaction. Flow cytometry were performed to measure the apoptosis of lentivial-transfected MM1R cells. Western blot analysis was performed to assess the apoptosis and signal transducer and activator of transcription 3 pathway-related factors. The results demonstrated that GRK6 was differentially expressed in individuals who suffered from MM and healthy individuals. Previous studies have shown that downregulating GRK6 has anti-cancer effects in the MM cell line, MM1R. The present study demonstrated that RNA interference-mediated GRK6 knockdown promoted apoptosis in the MM1R cell line. Therefore, we hypothesized that GRK6 plays a significant role in determining the course of MM.
Collapse
Affiliation(s)
- Zhiyao Zhang
- Department of Hematology, Beijing Chao Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Zhenyu Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu 221002, P.R. China
| | - Wenming Chen
- Department of Hematology, Beijing Chao Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| |
Collapse
|
23
|
Verkhivker GM. Biophysical simulations and structure-based modeling of residue interaction networks in the tumor suppressor proteins reveal functional role of cancer mutation hotspots in molecular communication. Biochim Biophys Acta Gen Subj 2018; 1863:210-225. [PMID: 30339916 DOI: 10.1016/j.bbagen.2018.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/19/2022]
Abstract
In the current study, we have combined molecular simulations and energetic analysis with dynamics-based network modeling and perturbation response scanning to determine molecular signatures of mutational hotspot residues in the p53, PTEN, and SMAD4 tumor suppressor proteins. By examining structure, energetics and dynamics of these proteins, we have shown that inactivating mutations preferentially target a group of structurally stable residues that play a fundamental role in global propagation of dynamic fluctuations and mediating allosteric interaction networks. Through integration of long-range perturbation dynamics and network-based approaches, we have quantified allosteric potential of residues in the studied proteins. The results have revealed that mutational hotspot sites often correspond to high centrality mediating centers of the residue interaction networks that are responsible for coordination of global dynamic changes and allosteric signaling. Our findings have also suggested that structurally stable mutational hotpots can act as major effectors of allosteric interactions and mutations in these positions are typically associated with severe phenotype. Modeling of shortest inter-residue pathways has shown that mutational hotspot sites can also serve as key mediating bridges of allosteric communication in the p53 and PTEN protein structures. Multiple regression models have indicated that functional significance of mutational hotspots can be strongly associated with the network signatures serving as robust predictors of critical regulatory positions responsible for loss-of-function phenotype. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of mutational hotspots, providing a plausible rationale for explaining and localizing disease-causing mutations in tumor suppressor genes.
Collapse
Affiliation(s)
- Gennady M Verkhivker
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| |
Collapse
|
24
|
Xin Z, Song X, Jiang B, Gongsun X, Song L, Qin Q, Wang Q, Shi M, Liu X. Blocking FGFR4 exerts distinct anti-tumorigenic effects in esophageal squamous cell carcinoma. Thorac Cancer 2018; 9:1687-1698. [PMID: 30267473 PMCID: PMC6275831 DOI: 10.1111/1759-7714.12883] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
Background The FGFR family can be activated by FGFs and plays important roles in regulating cell growth, differentiation, migration, and angiogenesis. Recent studies have suggested that FGFR4 could regulate several processes, including tumor progression. Esophageal squamous cell carcinoma (ESCC) is a malignancy with high global occurrence. However, the molecule mechanism and the potential roles of FGFR4 in ESCC remain unknown. Methods Immunohistochemistry and Western blotting were used to detect FGFR4 expression in ESCC samples and cell lines. Cell counting kit‐8, and clonogenic, transwell, flow cytometric, and tumor xenograft in nude mice assays were utilized to determine the effect of blocking FGFR4 in proliferation, invasion, migration, and apoptosis of ESCC cells. Results FGFR4 is frequently overexpressed in ESCC tissue and cell lines. in vitro assays have shown that blocking FGFR4 by a specific blocker, H3B‐6527, significantly decreases proliferation, invasion, and migration, and alters epithelial‐mesenchymal transition markers in ESCC cells. In addition, FGFR4 blockade is associated with the induction of apoptosis and affects PI3K/Akt and MAPK/ERK pathways. Moreover, FGFR4 blockade could significantly inhibit the growth of xenograft tumors in vivo. Conclusion Our findings suggest that blocking FGFR4 significantly suppresses the malignant behaviors of ESCC and indicate that FGFR4 is a potential target for the treatment of ESCC.
Collapse
Affiliation(s)
- Zhongwei Xin
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Xuemin Song
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Bin Jiang
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Xin Gongsun
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Liang Song
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Qiming Qin
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Qiang Wang
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Mo Shi
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Xiangyan Liu
- Department of Thoracic Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| |
Collapse
|
25
|
Agajanian S, Odeyemi O, Bischoff N, Ratra S, Verkhivker GM. Machine Learning Classification and Structure–Functional Analysis of Cancer Mutations Reveal Unique Dynamic and Network Signatures of Driver Sites in Oncogenes and Tumor Suppressor Genes. J Chem Inf Model 2018; 58:2131-2150. [DOI: 10.1021/acs.jcim.8b00414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Steve Agajanian
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Oluyemi Odeyemi
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Nathaniel Bischoff
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Simrath Ratra
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
- Chapman University, School of Pharmacy, Irvine, California 92618, United States
| |
Collapse
|
26
|
Kallus S, Englinger B, Senkiv J, Laemmerer A, Heffeter P, Berger W, Kowol CR, Keppler BK. Nanoformulations of anticancer FGFR inhibitors with improved therapeutic index. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:2632-2643. [PMID: 30121385 DOI: 10.1016/j.nano.2018.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 06/25/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023]
Abstract
Fibroblast growth factor receptor (FGFR) inhibitors like ponatinib and nintedanib are clinically approved for defined cancer patient cohorts but often exert dose-limiting adverse effects. Hence, we encapsulated the FGFR inhibitors ponatinib, PD173074, and nintedanib into polylactic acid nanoparticles and liposomes to enable increased tumor accumulation/specificity and reduce side effects. Different methods of drug loading were tested and the resulting formulations compared regarding average size distribution as well as encapsulation efficiency. Appropriate encapsulation levels were achieved for liposomal preparations only. Nanoencapsulation resulted in significantly decelerated uptake kinetics in vitro with clearly decreased short-term (up to 72 h) cytotoxicity at higher concentrations. However, in long-term clonogenic assays liposomal formations were equally or even more active as compared to the free drugs. Accordingly, in an FGFR inhibitor-sensitive murine osteosarcoma transplantation model (K7M2), only liposomal but not free ponatinib resulted in significant tumor growth inhibition (by 60.4%) at markedly reduced side effects.
Collapse
Affiliation(s)
- Sebastian Kallus
- University of Vienna, Faculty of Chemistry, Institute of Inorganic Chemistry, Vienna, Austria
| | - Bernhard Englinger
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Julia Senkiv
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Institute of Cell Biology of National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Anna Laemmerer
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Petra Heffeter
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", Vienna, Austria.
| | - Christian R Kowol
- University of Vienna, Faculty of Chemistry, Institute of Inorganic Chemistry, Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", Vienna, Austria.
| | - Bernhard K Keppler
- University of Vienna, Faculty of Chemistry, Institute of Inorganic Chemistry, Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", Vienna, Austria
| |
Collapse
|
27
|
Jiang Z, Yang Z, Li F, Li Z, Fishkin N, Burgess K. Targeted Maytansinoid Conjugate Improves Therapeutic Index for Metastatic Breast Cancer Cells. Bioconjug Chem 2018; 29:2920-2926. [DOI: 10.1021/acs.bioconjchem.8b00340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhengyang Jiang
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zhen Yang
- Center for Bioenergetics, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
| | - Feng Li
- Center for Bioenergetics, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
| | - Zheng Li
- Center for Bioenergetics, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
| | - Nathan Fishkin
- ImmunoGen, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| |
Collapse
|
28
|
Fujiki Y, Yamamoto Y, Sueta A, Yamamoto-Ibusuki M, Goto-Yamaguchi L, Tomiguchi M, Takeshita T, Iwase H. APOBEC3B gene expression as a novel predictive factor for pathological complete response to neoadjuvant chemotherapy in breast cancer. Oncotarget 2018; 9:30513-30526. [PMID: 30093965 PMCID: PMC6078135 DOI: 10.18632/oncotarget.25495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 05/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3B (APOBEC3B) is a gene editing enzyme with cytidine deaminase activity and high expression of its mRNA in breast tumors have been shown to be associated with progressive cases and poor prognosis. In this study, we aimed to examine the relationship between the expression of APOBEC3B and the effect of neoadjuvant chemotherapy (NAC) using pretreatment biopsy tissue, and examined whether the expression of APOBEC3B influenced chemotherapy efficacy. Methods We retrospectively selected a total of 274 patients with primary breast cancer who received NAC in more than 4 courses and underwent surgery at our institute. We assessed the expression of APOBEC3B mRNA using pretreatment biopsy specimens of NAC by quantitative real-time PCR (qRT-PCR) and examined the relationship between APOBEC3B mRNA expression and sensitivity to chemotherapy using pathological complete response (pCR) as an indicator. Further, we assessed the prognostic value of APOBEC3B in the patients receiving NAC. Results APOBEC3B mRNA expression levels were successfully assessed in 173 (63.1%) of the 274 specimens. The total pCR rate was 36.4% (n = 63). An association between APOBEC3B expression levels and pCR was observed (Wilcoxon test, P ≤ 0.0001). The patients were divided into two groups, low (n = 66) and high (n = 107), according to the APOBEC3B expression levels, using the cut-off value calculated by the receiver operating characteristics (ROC) curve for pCR. The rate of pCR was significantly higher among the patients in the high group than among those in the low group (47.7% vs 18.2%, P ≤ 0.0001). High APOBEC3B expression was significantly associated with high nuclear grade (P = 0.0078), high Ki-67 labeling index (P = 0.0087), estrogen receptor (ER) negativity (P ≤ 0.0001) and human epidermal growth factor receptor 2 (HER2) negativity (P = 0.032). Tumor size (P = 0.011), ER (P ≤ 0.0001), HER2 (P = 0.0013) and APOBEC3B expression (P = 0.037) were independent predictive factors for pCR in multivariate analysis. However, there was no association between APOBEC3B expression and prognosis. Conclusions Our study showed that APOBEC3B mRNA expression correlated with sensitivity to NAC in breast cancer patients. In contrast to previous studies, APOBEC3B mRNA expression was not associated with breast cancer prognosis in patients receiving NAC.
Collapse
Affiliation(s)
- Yoshitaka Fujiki
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Yutaka Yamamoto
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Aiko Sueta
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Mutsuko Yamamoto-Ibusuki
- Department of Molecular-Targeting Therapy for Breast Cancer, Kumamoto University Hospital, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Lisa Goto-Yamaguchi
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Mai Tomiguchi
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Takashi Takeshita
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| |
Collapse
|
29
|
The Nogo receptor inhibits proliferation, migration and axonal extension by transcriptionally regulating WNK1 in PC12 cells. Neuroreport 2018; 28:533-539. [PMID: 28489665 DOI: 10.1097/wnr.0000000000000800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Neuronal regeneration and axonal regrowth mechanisms in the injured mammalian central nervous system are largely unknown. As part of a major pathway for inhibiting axonal regeneration, activated neuronal glycosylphosphatidylinositol-anchored Nogo receptor (NgR) interacts with LINGO-1 and p75NTR to form a complex at the cell surface. However, it was found in our previous report that upregulation of NgR stimulated by injury plays a key role in neuronal regeneration in the neonatal cortex freeze-lesion model, but its downstream signalling remains elusive. In the present study, the novel regulatory role of NgR in a serine-threonine kinase WNK1 was identified. NgR's transcriptional regulation of WNK1 was identified by RT-qPCR and semiquantitative western blot after the overexpression or knockdown of NgR, and the regulation is specific to WNK1, which is not the same for its family members, WNK2, WNK3 and WNK4. Furthermore, NgR inhibition by NEP fails to affect WNK1, which indicates that WNK1 functions outside of the Nogo-A/NgR pathway. By performing a proliferation, migration and axonal extension assay, we also identified that overexpressed NgR critically regulated these processes and impairment by overexpressing NgR was rescued with coexpression of WNK1, indicating the partial role of WNK1 in NgR-mediated morphological regulation. Our study identifies a separation of functions for the NgR-regulated WNK1 in mediating proliferation, migration and axonal extension in PC12 cells as well as a specific regulatory role between NgR and WNK1 that is important for recovery from central nervous system injury.
Collapse
|
30
|
Mishra R, Hanker AB, Garrett JT. Genomic alterations of ERBB receptors in cancer: clinical implications. Oncotarget 2017; 8:114371-114392. [PMID: 29371993 PMCID: PMC5768410 DOI: 10.18632/oncotarget.22825] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/09/2017] [Indexed: 12/28/2022] Open
Abstract
The ERBB family of receptor tyrosine kinases has been implicated in carcinogenesis for over three decades with rigorous attention to EGFR and HER2. ERBB receptors, consisting of EGFR, HER2, HER3, and HER4 are part of a complicated signaling network that activates downstream signaling pathways including PI3K/AKT, Ras/Raf/MAPK, JAK/STAT and PKC. It is well established that EGFR is amplified and/or mutated in gliomas and non-small-cell lung carcinoma while HER2 is amplified and/or over-expressed in breast, gastric, ovarian, non-small cell lung carcinoma, and several other tumor types. With the advent of next generation sequencing and large scale efforts to explore the entire spectrum of genomic alterations involved in human cancer progression, it is now appreciated that somatic ERBB receptor mutations occur at relatively low frequencies across multiple tumor types. Some of these mutations may represent oncogenic driver events; clinical studies are underway to determine whether tumors harboring these alterations respond to small molecule EGFR/HER2 inhibitors. Recent evidence suggests that some somatic ERBB receptor mutations render resistance to FDA-approved EGFR and HER2 inhibitors. In this review, we focus on the landscape of genomic alterations of EGFR, HER2, HER3 and HER4 in cancer and the clinical implications for patients harboring these alterations.
Collapse
Affiliation(s)
- Rosalin Mishra
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio, U.S.A
| | - Ariella B Hanker
- Department of Medicine, Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, U.S.A
| | - Joan T Garrett
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio, U.S.A
| |
Collapse
|
31
|
Soady KJ, Tornillo G, Kendrick H, Meniel V, Olijnyk-Dallis D, Morris JS, Stein T, Gusterson BA, Isacke CM, Smalley MJ. The receptor protein tyrosine phosphatase PTPRB negatively regulates FGF2-dependent branching morphogenesis. Development 2017; 144:3777-3788. [PMID: 28870991 PMCID: PMC6126639 DOI: 10.1242/dev.149120] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 08/25/2017] [Indexed: 02/02/2023]
Abstract
PTPRB is a transmembrane protein tyrosine phosphatase known to regulate blood vessel remodelling and angiogenesis. Here, we demonstrate that PTPRB negatively regulates branching morphogenesis in the mouse mammary epithelium. We show that Ptprb is highly expressed in adult mammary stem cells and also, although at lower levels, in oestrogen receptor-positive luminal cells. During mammary development, Ptprb expression is downregulated during puberty, a period of extensive ductal outgrowth and branching. In vivo shRNA knockdown of Ptprb in the cleared mammary fat pad transplant assay resulted in smaller epithelial outgrowths with an increased branching density and also increased branching in an in vitro organoid assay. Organoid branching was dependent on stimulation by FGF2, and Ptprb knockdown in mammary epithelial cells resulted in a higher level of fibroblast growth factor receptor (FGFR) activation and ERK1/2 phosphorylation, both at baseline and following FGF2 stimulation. Therefore, PTPRB regulates branching morphogenesis in the mammary epithelium by modulating the response of the FGFR signalling pathway to FGF stimulation. Considering the importance of branching morphogenesis in multiple taxa, our findings have general importance outside mammary developmental biology.
Collapse
Affiliation(s)
- Kelly J Soady
- Division of Breast Cancer Research, Breast Cancer Now Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Giusy Tornillo
- European Cancer Stem Cell Research Institute and Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Howard Kendrick
- European Cancer Stem Cell Research Institute and Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Valerie Meniel
- European Cancer Stem Cell Research Institute and Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Daria Olijnyk-Dallis
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Joanna S Morris
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK
| | - Torsten Stein
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Barry A Gusterson
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Clare M Isacke
- Division of Breast Cancer Research, Breast Cancer Now Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Matthew J Smalley
- European Cancer Stem Cell Research Institute and Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| |
Collapse
|
32
|
Kamkaew A, Li F, Li Z, Burgess K. An agent for optical imaging of TrkC-expressing, breast cancer. MEDCHEMCOMM 2017; 8:1946-1952. [PMID: 30108715 DOI: 10.1039/c7md00328e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/17/2017] [Indexed: 11/21/2022]
Abstract
Tropomyosin receptor kinases receptor C is expressed at high levels on the surface of tumors from metastatic breast cancer, metastatic melanoma, glioblastoma, and neuroblastoma. Previous studies have shown synthetic TrkC ligands bearing agents for photodynamic therapy could be used to completely ablate 4T1 metastatic breast tumors and suppress metastatic spread in vivo. Modification of these probes (A in the text) to make them suitable for near infrared optical imaging in vivo would require a substantial increase in molecular mass (and hence increased vulnerability to undesirable absorption, metabolism and immunogenicity effects), or significant changes to the probe design which might compromise binding to TrkC in histochemical studies and on live cells. The research featured here was undertaken to investigate if the second strategy could be achieved without compromising binding to TrkC-expressing tissues. Specifically, an "aza-BODIPY" probe was synthesized to replace a spacer fragment in the original probe A. In the event, this new probe design (1a in the text) binds TrkC+ breast cancer in live cell cultures, in histochemical studies and in an in vivo murine model. Probe 1a binds TrkC+ tissues with good contrast with respect to healthy tissues, and much more strongly than an isomeric, non-TrkC binding, probe (1b) prepared as a negative control.
Collapse
Affiliation(s)
- Anyanee Kamkaew
- Department of Chemistry , Texas A & M University , Box 30012, College Station , TX 77842 , USA . .,School of Chemistry , Institute of Science , Suranaree University of Technology , Nakhon Ratchasima 30000 , Thailand
| | - Feng Li
- Center for Bioenergetics , Houston Methodist Research Institute , Houston , TX 77030 , USA .
| | - Zheng Li
- Center for Bioenergetics , Houston Methodist Research Institute , Houston , TX 77030 , USA .
| | - Kevin Burgess
- Department of Chemistry , Texas A & M University , Box 30012, College Station , TX 77842 , USA .
| |
Collapse
|
33
|
Lei H, Deng CX. Fibroblast Growth Factor Receptor 2 Signaling in Breast Cancer. Int J Biol Sci 2017; 13:1163-1171. [PMID: 29104507 PMCID: PMC5666331 DOI: 10.7150/ijbs.20792] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 05/18/2017] [Indexed: 01/03/2023] Open
Abstract
Fibroblast growth factor receptor 2 (FGFR2) is a membrane-spanning tyrosine kinase that mediates signaling for FGFs. Recent studies detected various point mutations of FGFR2 in multiple types of cancers, including breast cancer, lung cancer, gastric cancer, uterine cancer and ovarian cancer, yet the casual relationship between these mutations and tumorigenesis is unclear. Here we will discuss possible interactions between FGFR2 signaling and several major pathways through which the aberrantly activated FGFR2 signaling may result in breast cancer development. We will also discuss some recent developments in the discovery and application of therapies and strategies for breast cancers by inhibiting FGFR2 activities.
Collapse
Affiliation(s)
- Haipeng Lei
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| |
Collapse
|
34
|
Banister CE, Liu C, Pirisi L, Creek KE, Buckhaults PJ. Identification and characterization of HPV-independent cervical cancers. Oncotarget 2017; 8:13375-13386. [PMID: 28077784 PMCID: PMC5355105 DOI: 10.18632/oncotarget.14533] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/27/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) initiates cervical cancer, and continuous expression of HPV oncogenes E6 and E7 is thought to be necessary to maintain malignant growth. Current therapies target proliferating cells, rather than specific pathways, and most experimental therapies specifically target E6/E7. We investigated the presence and expression of HPV in cervical cancer, to correlate HPV oncogene expression with clinical and molecular features of these tumors that may be relevant to new targeted therapies. RESULTS While virtually all cervical cancers contained HPV DNA, and most expressed E6/E7 (HPV-active), a subset (8%) of HPV DNA-positive cervical cancers did not express HPV transcripts (HPV-inactive). HPV-inactive tumors occurred in older women (median 54 vs. 45 years, p = 0.02) and were associated with poorer survival (median 715 vs 3046 days, p = 0.0003). Gene expression profiles of HPV-active and -inactive tumors were distinct. HPV-active tumors expressed E2F target genes and increased AKT/MTOR signaling. HPV-inactive tumors had increased WNT/β-catenin and Sonic Hedgehog signaling. Substantial genome-wide differences in DNA methylation were observed. HPV-inactive tumors had a global decrease in DNA methylation; however, many promoter-associated CpGs were hypermethylated. Many inflammatory response genes showed promoter methylation and decreased expression. The somatic mutation landscapes were significantly different. HPV-active tumors carried few somatic mutations in driver genes, whereas HPV-inactive tumors were enriched for non-synonymous somatic mutations (p-value < 0.0000001) specifically targeting TP53, ARID, WNT, and PI3K pathways. MATERIALS AND METHODS The Cancer Genome Atlas (TCGA) cervical cancer data were analyzed. CONCLUSIONS Many of the gene expression changes and somatic mutations found in HPV-inactive tumors alter pathways for which targeted therapeutics are available. Treatment strategies focused on WNT, PI3K, or TP53 mutations may be effective against HPV-inactive tumors and could improve survival for these cervical cancer patients.
Collapse
Affiliation(s)
| | - Changlong Liu
- University of South Carolina College of Pharmacy, Columbia, SC, USA
| | - Lucia Pirisi
- University of South Carolina School of Medicine, Columbia, SC, USA
| | - Kim E Creek
- University of South Carolina College of Pharmacy, Columbia, SC, USA
| | | |
Collapse
|
35
|
Yang B, Li X, Lei L, Chen J. APOBEC: From mutator to editor. J Genet Genomics 2017; 44:423-437. [PMID: 28964683 DOI: 10.1016/j.jgg.2017.04.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Abstract
APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) are a family of cytidine deaminases that prefer single-stranded nucleic acids as substrates. Besides their physiological functions, APOBEC family members have been found to cause hypermutations of cancer genomes, which could be correlated with cancer development and poor prognosis. Recently, APOBEC family members have been combined with the versatile CRISPR/Cas9 system to perform targeted base editing or induce hypermutagenesis. This combination improved the CRISPR/Cas9-mediated gene editing at single-base precision, greatly enhancing its usefulness. Here, we review the physiological functions and structural characteristics of APOBEC family members and their roles as endogenous mutators that contribute to hypermutations during carcinogenesis. We also review the various iterations of the APOBEC-CRISPR/Cas9 gene-editing tools, pointing out their features and limitations as well as the possibilities for future developments.
Collapse
Affiliation(s)
- Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Xiaosa Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Liqun Lei
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jia Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| |
Collapse
|
36
|
Characterization and enzymatic properties of protein kinase ACR4 from Arabidopsis thaliana. Biochem Biophys Res Commun 2017; 489:270-274. [PMID: 28571742 DOI: 10.1016/j.bbrc.2017.05.163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/28/2017] [Indexed: 01/04/2023]
Abstract
Serine/threonine-protein kinase-like protein ARABIDOPSIS CRINKLY4 (ACR4), a transmembrane protein of Arabidopsis thaliana, plays important roles in cell division and differentiation. Although accumulating studies shed light on the function of ACR4, the structure and catalytic mechanism of ACR4 remain to be elucidated. Here, we report the purification and enzymatic properties of the intracellular kinase domain (residues 464-799) of ACR4 (ACR4IKD). Through Ni-affinity chromatography and gel filter chromatography methods, we successfully obtain high-purity ACR4IKD protein from Escherichia coli. Dynamic light scattering and gel-filtration methods reveal that ACR4IKD distributes with high homogeneity and exists as a monomer in solution. In addition, the ACR4IKD protein has typical kinase activity with myelin basic protein (MBP) as the substrate. Our study may lay the foundation for structure determination of ACR4IKD and further functional research, for example, screening significant substrates of ACR4 in Arabidopsis thaliana.
Collapse
|
37
|
Ardito F, Giuliani M, Perrone D, Troiano G, Lo Muzio L. The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review). Int J Mol Med 2017; 40:271-280. [PMID: 28656226 PMCID: PMC5500920 DOI: 10.3892/ijmm.2017.3036] [Citation(s) in RCA: 703] [Impact Index Per Article: 100.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
Protein phosphorylation is an important cellular regulatory mechanism as many enzymes and receptors are activated/deactivated by phosphorylation and dephosphorylation events, by means of kinases and phosphatases. In particular, the protein kinases are responsible for cellular transduction signaling and their hyperactivity, malfunction or overexpression can be found in several diseases, mostly tumors. Therefore, it is evident that the use of kinase inhibitors can be valuable for the treatment of cancer. In this review, we discuss the mechanism of action of phosphorylation, with particular attention to the importance of phosphorylation under physiological and pathological conditions. We also discuss the possibility of using kinase inhibitors in the treatment of tumors.
Collapse
Affiliation(s)
- Fatima Ardito
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Michele Giuliani
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Donatella Perrone
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| |
Collapse
|
38
|
Lok JB, Shao H, Massey HC, Li X. Transgenesis in Strongyloides and related parasitic nematodes: historical perspectives, current functional genomic applications and progress towards gene disruption and editing. Parasitology 2017; 144:327-342. [PMID: 27000743 PMCID: PMC5364836 DOI: 10.1017/s0031182016000391] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 12/20/2022]
Abstract
Transgenesis for Strongyloides and Parastrongyloides was accomplished in 2006 and is based on techniques derived for Caenorhabditis elegans over two decades earlier. Adaptation of these techniques has been possible because Strongyloides and related parasite genera carry out at least one generation of free-living development, with adult males and females residing in soil contaminated by feces from an infected host. Transgenesis in this group of parasites is accomplished by microinjecting DNA constructs into the syncytia of the distal gonads of free-living females. In Strongyloides stercoralis, plasmid-encoded transgenes are expressed in promoter-regulated fashion in the F1 generation following gene transfer but are silenced subsequently. Stable inheritance and expression of transgenes in S. stercoralis requires their integration into the genome, and stable lines have been derived from integrants created using the piggyBac transposon system. More direct investigations of gene function involving expression of mutant transgene constructs designed to alter intracellular trafficking and developmental regulation have shed light on the function of the insulin-regulated transcription factor Ss-DAF-16. Transgenesis in Strongyloides and Parastrongyloides opens the possibility of powerful new methods for genome editing and transcriptional manipulation in this group of parasites. Proof of principle for one of these, CRISPR/Cas9, is presented in this review.
Collapse
Affiliation(s)
- J B Lok
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
| | - H Shao
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
| | - H C Massey
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
| | - X Li
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
| |
Collapse
|
39
|
Xie X, Wang Z, Chen F, Yuan Y, Wang J, Liu R, Chen Q. Roles of FGFR in oral carcinogenesis. Cell Prolif 2017; 49:261-9. [PMID: 27218663 DOI: 10.1111/cpr.12260] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) play essential roles in organ development during the embryonic period, and regulate tissue repair in adults. Accumulating evidence suggests that alterations in FGFR signalling are involved in diverse types of cancer. In this review, we focus on aberrant regulation of FGFRs in pathogenesis of oral squamous cell carcinoma (OSCC), including altered expression and subcellular location, aberrant isoform splicing and mutations. We also provide an overview of oncogenic roles of each FGFR and its downstream signalling pathways in regulating OSCC cell proliferation and metastasis. Finally, we discuss potential application of FGFRs as anti-cancer targets in the preclinical environment and in clinical practice.
Collapse
Affiliation(s)
- Xiaoyan Xie
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Fangman Chen
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yao Yuan
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jiayi Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Rui Liu
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| |
Collapse
|
40
|
Ruan Z, Katiyar S, Kannan N. Computational and Experimental Characterization of Patient Derived Mutations Reveal an Unusual Mode of Regulatory Spine Assembly and Drug Sensitivity in EGFR Kinase. Biochemistry 2017; 56:22-32. [PMID: 27936599 PMCID: PMC5508873 DOI: 10.1021/acs.biochem.6b00572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The catalytic activation of protein kinases requires precise positioning of key conserved catalytic and regulatory motifs in the kinase core. The Regulatory Spine (RS) is one such structural motif that is dynamically assembled upon kinase activation. The RS is also a mutational hotspot in cancers; however, the mechanisms by which cancer mutations impact RS assembly and kinase activity are not fully understood. In this study, through mutational analysis of patient derived mutations in the RS of EGFR kinase, we identify an activating mutation, M766T, at the RS3 position. RS3 is located in the regulatory αC-helix, and a series of mutations at the RS3 position suggest a strong correlation between the amino acid type present at the RS3 position and ligand (EGF) independent EGFR activation. Small polar amino acids increase ligand independent activity, while large aromatic amino acids decrease kinase activity. M766T relies on the canonical asymmetric dimer for full activation. Molecular modeling and molecular dynamics simulations of WT and mutant EGFR suggest a model in which M766T activates the kinase domain by disrupting conserved autoinhibitory interactions between M766 and hydrophobic residues in the activation segment. In addition, a water mediated hydrogen bond network between T766, the conserved K745-E762 salt bridge, and the backbone amide of the DFG motif is identified as a key determinant of M766T-mediated activation. M766T is resistant to FDA approved EGFR inhibitors such as gefitinib and erlotinib, and computational estimation of ligand binding free energy identifies key residues associated with drug sensitivity. In sum, our studies suggest an unusual mode of RS assembly and oncogenic EGFR activation, and provide new clues for the design of allosteric protein kinase inhibitors.
Collapse
Affiliation(s)
- Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Samiksha Katiyar
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
41
|
Walker CJ, Goodfellow PJ. Traditional Approaches to Molecular Genetic Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 943:99-118. [DOI: 10.1007/978-3-319-43139-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
42
|
Kim MS, Jeong J, Seo J, Kim HS, Kim SJ, Jin W. Dysregulated JAK2 expression by TrkC promotes metastasis potential, and EMT program of metastatic breast cancer. Sci Rep 2016; 6:33899. [PMID: 27654855 PMCID: PMC5032000 DOI: 10.1038/srep33899] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/02/2016] [Indexed: 12/22/2022] Open
Abstract
Metastatic breast cancers are aggressive tumors associated with high levels of epithelial-mesenchymal transition (EMT) markers, activation of IL6/JAK2/STAT3 and PI3K/AKT pathways for cell growth, mobility, invasion, metastasis, and CSC status. We identified a new molecular and functional network present in metastasis that regulates and coordinates with TrkC. Inhibition of SOCS3-mediated JAK2 degradation by TrkC increases total JAK2/STAT3 expression, and then leads to upregulation of Twist-1 through activation of JAK2/STAT3 cascade. Also, TrkC increases secretion and expression of IL-6, suggesting that this autocrine loop generated by TrkC maintains the mesenchymal state by continued activation of the JAK2/STAT3 cascade and upregulation of Twist expression. Moreover, TrkC interacts with the c-Src/Jak2 complex, which increases Twist-1 and Twist-2 levels via regulation of JAK2/STAT3 activation and JAK2/STAT3 expression. Furthermore, TrkC enhances metastatic potential of breast cancer via induction of EMT by upregulating Twist-1 and Twist-2. Additionally, TrkC significantly enhances the ability of breast cancer cells to form pulmonary metastases and primary tumor formation. Unexpectedly, we found that TrkC expression and clinical breast tumor pathological phenotypes show significant correlation. These findings suggest that TrkC plays a central role in tumorigenicity, metastasis, and self-renewal traits of metastatic breast cancer.
Collapse
Affiliation(s)
- Min Soo Kim
- Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon 406-840, Korea
| | - Joon Jeong
- Department of Surgery, Gangnam Severance Hospital, Yonsei University Medical College, 712 Eonjuro, Gangnam-Gu, Seoul, 135-720, Korea
| | - Jeongbeob Seo
- Medicinal Chemistry, CMG Pharma, 335, CHA Bio Complex, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, Korea
| | - Hae-Suk Kim
- TheragenEtex Bio Institute, TheragenEtex Co., Suwon, Gyeonggi-do 16229, Republic of Korea
| | - Seong-Jin Kim
- Nano-Bio Medicine Research Center, Advanced Institutes of Convergence Technology, and Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Kyunggi-do 16229, Republic of Korea
| | - Wook Jin
- Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon 406-840, Korea.,Gachon Medical Research Institute, Gil Medical Center, Incheon, 405-760, Korea
| |
Collapse
|
43
|
Wu D, Guo M, Philips MA, Qu L, Jiang L, Li J, Chen X, Chen Z, Chen L, Chen Y. Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455. PLoS One 2016; 11:e0162491. [PMID: 27618313 PMCID: PMC5019380 DOI: 10.1371/journal.pone.0162491] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/23/2016] [Indexed: 12/29/2022] Open
Abstract
Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.
Collapse
Affiliation(s)
- Daichao Wu
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ming Guo
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
| | - Michael A. Philips
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States of America
| | - Lingzhi Qu
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
| | - Longying Jiang
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lin Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States of America
- * E-mail: (YC); (LC)
| | - Yongheng Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States of America
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, Guangdong, China
- * E-mail: (YC); (LC)
| |
Collapse
|
44
|
Mishra PK, Ciftci-Yilmaz S, Reynolds D, Au WC, Boeckmann L, Dittman LE, Jowhar Z, Pachpor T, Yeh E, Baker RE, Hoyt MA, D'Amours D, Bloom K, Basrai MA. Polo kinase Cdc5 associates with centromeres to facilitate the removal of centromeric cohesin during mitosis. Mol Biol Cell 2016; 27:2286-300. [PMID: 27226485 PMCID: PMC4945145 DOI: 10.1091/mbc.e16-01-0004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/27/2016] [Accepted: 05/19/2016] [Indexed: 12/20/2022] Open
Abstract
Sister chromatid cohesion is essential for tension-sensing mechanisms that monitor bipolar attachment of replicated chromatids in metaphase. Cohesion is mediated by the association of cohesins along the length of sister chromatid arms. In contrast, centromeric cohesin generates intrastrand cohesion and sister centromeres, while highly cohesin enriched, are separated by >800 nm at metaphase in yeast. Removal of cohesin is necessary for sister chromatid separation during anaphase, and this is regulated by evolutionarily conserved polo-like kinase (Cdc5 in yeast, Plk1 in humans). Here we address how high levels of cohesins at centromeric chromatin are removed. Cdc5 associates with centromeric chromatin and cohesin-associated regions. Maximum enrichment of Cdc5 in centromeric chromatin occurs during the metaphase-to-anaphase transition and coincides with the removal of chromosome-associated cohesin. Cdc5 interacts with cohesin in vivo, and cohesin is required for association of Cdc5 at centromeric chromatin. Cohesin removal from centromeric chromatin requires Cdc5 but removal at distal chromosomal arm sites does not. Our results define a novel role for Cdc5 in regulating removal of centromeric cohesins and faithful chromosome segregation.
Collapse
Affiliation(s)
- Prashant K Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Sultan Ciftci-Yilmaz
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - David Reynolds
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lauren E Dittman
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ziad Jowhar
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tejaswini Pachpor
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elaine Yeh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - M Andrew Hoyt
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Damien D'Amours
- Institute for Research in Immunology and Cancer and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Munira A Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
45
|
Byeon IJL, Byeon CH, Wu T, Mitra M, Singer D, Levin JG, Gronenborn AM. Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity. Biochemistry 2016; 55:2944-59. [PMID: 27163633 DOI: 10.1021/acs.biochem.6b00382] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Human APOBEC3B (A3B) is a member of the APOBEC3 (A3) family of cytidine deaminases, which function as DNA mutators and restrict viral pathogens and endogenous retrotransposons. Recently, A3B was identified as a major source of genetic heterogeneity in several human cancers. Here, we determined the solution nuclear magnetic resonance structure of the catalytically active C-terminal domain (CTD) of A3B and performed detailed analyses of its deaminase activity. The core of the structure comprises a central five-stranded β-sheet with six surrounding helices, common to all A3 proteins. The structural fold is most similar to that of A3A and A3G-CTD, with the most prominent difference being found in loop 1. The catalytic activity of A3B-CTD is ∼15-fold lower than that of A3A, although both exhibit a similar pH dependence. Interestingly, A3B-CTD with an A3A loop 1 substitution had significantly increased deaminase activity, while a single-residue change (H29R) in A3A loop 1 reduced A3A activity to the level seen with A3B-CTD. This establishes that loop 1 plays an important role in A3-catalyzed deamination by precisely positioning the deamination-targeted C into the active site. Overall, our data provide important insights into the determinants of the activities of individual A3 proteins and facilitate understanding of their biological function.
Collapse
Affiliation(s)
| | | | - Tiyun Wu
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Mithun Mitra
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Dustin Singer
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Judith G Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | | |
Collapse
|
46
|
Petljak M, Alexandrov LB. Understanding mutagenesis through delineation of mutational signatures in human cancer. Carcinogenesis 2016; 37:531-40. [DOI: 10.1093/carcin/bgw055] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/29/2016] [Indexed: 01/04/2023] Open
|
47
|
FHIT loss-induced DNA damage creates optimal APOBEC substrates: Insights into APOBEC-mediated mutagenesis. Oncotarget 2016; 6:3409-19. [PMID: 25401976 PMCID: PMC4413662 DOI: 10.18632/oncotarget.2636] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/23/2014] [Indexed: 12/20/2022] Open
Abstract
APOBEC cytidine deaminase activity is a major source of hypermutation in cancer. But previous studies have shown that the TC context signature of these enzymes is not observed in sizable fractions of cancers with overexpression of APOBEC, suggesting that cooperating factors that contribute to this mutagenesis should be identified. The fragile histidine triad protein (Fhit) is a tumor suppressor and DNA caretaker that is deleted or silenced in >50% of cancers. Loss of Fhit protein activity causes replication stress through reduced Thymidine Kinase 1 expression, increased DNA breaks, and global genome instability in normal and cancer cells. Using data from The Cancer Genome Atlas (TCGA), we show that FHIT-low/APOBEC3B-high expressing lung adenocarcinomas display significantly increased numbers of APOBEC signature mutations. Tumor samples in this cohort with normal FHIT expression do not exhibit APOBEC hypermutation, despite having high APOBEC3B expression. In vitro, silencing Fhit expression elevates APOBEC3B-directed C > T mutations in the TP53 gene. Furthermore, inhibition of Fhit loss-induced DNA damage via thymidine supplementation decreases the TP53 mutation burden in FHIT-low/APOBEC3B-high cells. We conclude that APOBEC3B overexpression and Fhit-loss induced DNA damage are independent events that, when occurring together, result in a significantly increased frequency of APOBEC-induced mutations that drive cancer progression.
Collapse
|
48
|
Marouf C, Göhler S, Filho MIDS, Hajji O, Hemminki K, Nadifi S, Försti A. Analysis of functional germline variants in APOBEC3 and driver genes on breast cancer risk in Moroccan study population. BMC Cancer 2016; 16:165. [PMID: 26920143 PMCID: PMC4768349 DOI: 10.1186/s12885-016-2210-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/21/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most prevalent cancer in women and a major public health problem in Morocco. Several Moroccan studies have focused on studying this disease, but more are needed, especially at the genetic and molecular levels. Therefore, we investigated the potential association of several functional germline variants in the genes commonly mutated in sporadic breast cancer. METHODS In this case-control study, we examined 36 single nucleotide polymorphisms (SNPs) in 13 genes (APOBEC3A, APOBEC3B, ARID1B, ATR, MAP3K1, MLL2, MLL3, NCOR1, RUNX1, SF3B1, SMAD4, TBX3, TTN), which were located in the core promoter, 5'-and 3'UTR or which were nonsynonymous SNPs to assess their potential association with inherited predisposition to breast cancer development. Additionally, we identified a ~29.5-kb deletion polymorphism between APOBEC3A and APOBEC3B and explored possible associations with BC. A total of 226 Moroccan breast cancer cases and 200 matched healthy controls were included in this study. RESULTS The analysis showed that12 SNPs in 8 driver genes, 4 SNPs in APOBEC3B gene and 1 SNP in APOBEC3A gene were associated with BC risk and/or clinical outcome at P ≤ 0.05 level. RUNX1_rs8130963 (odds ratio (OR) = 2.25; 95 % CI 1.42-3.56; P = 0.0005; dominant model), TBX3_rs8853 (OR = 2.04; 95 % CI 1.38-3.01; P = 0.0003; dominant model), TBX3_rs1061651 (OR= 2.14; 95 % CI1.43-3.18; P = 0.0002; dominant model), TTN_rs12465459 (OR = 2.02; 95 % confidence interval 1.33-3.07; P = 0.0009; dominant model), were the most significantly associated SNPs with BC risk. A strong association with clinical outcome were detected for the genes SMAD4 _rs3819122 with tumor size (OR = 0.45; 95 % CI 0.25-0.82; P = 0.009) and TTN_rs2244492 with estrogen receptor (OR = 0.45; 95 % CI 0.25-0.82; P = 0.009). CONCLUSION Our results suggest that genetic variations in driver and APOBEC3 genes were associated with the risk of BC and may have impact on clinical outcome. However, the reported association between the deletion polymorphism and BC risk was not confirmed in the Moroccan population. These preliminary findings require replication in larger studies.
Collapse
Affiliation(s)
- Chaymaa Marouf
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Laboratory of Genetics and Molecular Pathology-Medical School of Casablanca, Casablanca, Morocco. .,University Hassan II Ain Chock, Center Of Doctoral Sciences "In Health Sciences", Casablanca, Morocco.
| | - Stella Göhler
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | | | - Omar Hajji
- Department of Oncology, Littoral Clinic, Casablanca, Morocco.
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
| | - Sellama Nadifi
- Laboratory of Genetics and Molecular Pathology-Medical School of Casablanca, Casablanca, Morocco. .,University Hassan II Ain Chock, Center Of Doctoral Sciences "In Health Sciences", Casablanca, Morocco.
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
| |
Collapse
|
49
|
Tong JH, Yeung SF, Chan AWH, Chung LY, Chau SL, Lung RWM, Tong CY, Chow C, Tin EKY, Yu YH, Li H, Pan Y, Chak WP, Ng CSH, Mok TSK, To KF. MET Amplification and Exon 14 Splice Site Mutation Define Unique Molecular Subgroups of Non-Small Cell Lung Carcinoma with Poor Prognosis. Clin Cancer Res 2016; 22:3048-56. [PMID: 26847053 DOI: 10.1158/1078-0432.ccr-15-2061] [Citation(s) in RCA: 323] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/16/2016] [Indexed: 12/12/2022]
Abstract
PURPOSE Activation of MET oncogene as the result of amplification or activation mutation represents an emerging molecular target for cancer treatment. We comprehensively studied MET alterations and the clinicopathologic correlations in a large cohort of treatment-naïve non-small cell lung carcinoma (NSCLC). EXPERIMENTAL DESIGN Six hundred eighty-seven NSCLCs were tested for MET exon 14 splicing site mutation (METΔ14), DNA copy number alterations, and protein expression by Sanger sequencing, FISH, and IHC, respectively. RESULTS METΔ14 mutation was detected in 2.62% (18/687) of NSCLC. The mutation rates were 2.6% in adenocarcinoma, 4.8% in adenosquamous carcinoma, and 31.8% in sarcomatoid carcinoma. METΔ14 mutation was not detected in squamous cell carcinoma, large cell carcinoma, and lymphoepithelioma-like carcinoma but significantly enriched in sarcomatoid carcinoma (P < 0.001). METΔ14 occurred mutually exclusively with known driver mutations but tended to coexist with MET amplification or copy number gain (P < 0.001). Low-level MET amplification and polysomy might occur in the background of EGFR or KRAS mutation whereas high-level amplification (MET/CEP7 ratio ≥5) was mutually exclusive to the major driver genes except METΔ14. Oncogenic METΔ14 mutation and/or high-level amplification occurred in a total of 3.3% (23/687) of NSCLC and associated with higher MET protein expression. METΔ14 occurred more frequently in older patients whereas amplification was more common in ever-smokers. Both METΔ14 and high-level amplification were independent prognostic factors that predicted poorer survival by multivariable analysis. CONCLUSIONS The high incidence of METΔ14 mutation in sarcomatoid carcinoma suggested that MET inhibition might benefit this specific subgroup of patients. Clin Cancer Res; 22(12); 3048-56. ©2016 AACRSee related commentary by Drilon, p. 2832.
Collapse
Affiliation(s)
- Joanna H Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Sai F Yeung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Anthony W H Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Lau Y Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Shuk L Chau
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Raymond Wai Ming Lung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Carol Y Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Chit Chow
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Edith K Y Tin
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Yau H Yu
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Hui Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Yi Pan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Wing P Chak
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Calvin S H Ng
- Division of Cardiothoracic Surgery, Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Tony S K Mok
- Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong. Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong
| | - Ka F To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong. State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong. Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong.
| |
Collapse
|
50
|
Novel mutations in neuroendocrine carcinoma of the breast: possible therapeutic targets. Appl Immunohistochem Mol Morphol 2015; 23:97-103. [PMID: 25679062 DOI: 10.1097/pdm.0b013e3182a40fd1] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Primary neuroendocrine carcinoma of the breast is a rare variant, accounting for only 2% to 5% of diagnosed breast cancers, and may have relatively aggressive behavior. Mutational profiling of invasive ductal breast cancers has yielded potential targets for directed cancer therapy, yet most studies have not included neuroendocrine carcinomas. In a tissue microarray screen, we found a 2.4% prevalence (9/372) of neuroendocrine breast carcinoma, including several with lobular morphology. We then screened primary or metastatic neuroendocrine breast carcinomas (excluding papillary and mucinous) for mutations in common cancer genes using polymerase chain reaction-mass spectroscopy (643 hotspot mutations across 53 genes), or semiconductor-based next-generation sequencing analysis (37 genes). Mutations were identified in 5 of 15 tumors, including 3 with PIK3CA exon 9 E542K mutations, 2 of which also harbored point mutations in FGFR family members (FGFR1 P126S, FGFR4 V550M). Single mutations were found in each of KDR (A1065T) and HRAS (G12A). PIK3CA mutations are common in other types of breast carcinoma. However, FGFR and RAS family mutations are exceedingly rare in the breast cancer literature. Likewise, activating mutations in the receptor tyrosine kinase KDR (VEGFR2) have been reported in angiosarcomas and non-small cell lung cancers; the KDR A1065T mutation is reported to be sensitive to VEGFR kinase inhibitors, and fibroblast growth factor receptor inhibitors are in trials. Our findings demonstrate the utility of broad-based genotyping in the study of rare tumors such as neuroendocrine breast cancer.
Collapse
|